Ch 5 Microbial Metabolism: Structured Study Notes

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all controlled biochemical reactions within a microbe, serving the ultimate function of reproducing the organism. It is divided into two major classes: catabolism and anabolism, which are interconnected through energy transfer and precursor molecules.

Catabolism: Breakdown of larger molecules into smaller products; exergonic (releases energy).
Anabolism: Synthesis of large molecules from smaller products; endergonic (requires energy).
ATP: Central molecule for energy storage and transfer.

Diagram of catabolism and anabolism in a cell

Additional info: Catabolic reactions provide energy and precursor metabolites for anabolic processes, which build cellular structures and macromolecules.

Catabolism and Anabolism

Catabolic and anabolic pathways are fundamental to cellular metabolism. Catabolic pathways release energy by breaking down complex molecules, while anabolic pathways consume energy to build complex molecules from simpler ones.

Catabolic Pathways: Exergonic, produce ATP and precursor metabolites.
Anabolic Pathways: Endergonic, use ATP and precursor metabolites to synthesize macromolecules.

Oxidation and Reduction Reactions

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

Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Electron Carriers: NAD+, NADP+, FAD.

Diagram of oxidation and reduction reactions

ATP Production and Energy Storage

Cells produce ATP by phosphorylating ADP through three mechanisms: substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation. ATP is then used to drive anabolic reactions.

Substrate-level phosphorylation: Direct transfer of phosphate to ADP.
Oxidative phosphorylation: Uses energy from electron transport chain.
Photophosphorylation: Uses light energy in photosynthetic organisms.

Enzymes in Metabolism

Enzyme Classification and Function

Enzymes are organic catalysts that increase the likelihood of biochemical reactions. They are classified 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 to fructose-6-phosphate during glycolysis
Ligase/Polymerase	Joining two or more chemicals together (anabolic)	Acetyl-CoA synthetase—combines acetate and coenzyme A to form acetyl-CoA for the Krebs cycle
Lyase	Splitting a chemical into smaller parts without using water	Fructose-1,6-bisphosphate aldolase—splits fructose-1,6-bisphosphate into G3P and DHAP during glycolysis
Oxidoreductase	Transfer of electrons or hydrogen atoms from one molecule to another	Lactic acid dehydrogenase—converts pyruvic acid to lactic acid during fermentation
Transferase	Moving a functional group from one molecule to another	Hexokinase—transfers phosphate from ATP to glucose in the first step of glycolysis

Table of enzyme classification based on reaction types

Enzyme Structure: Holoenzyme Components

Enzymes may require cofactors for activity. The combination of an apoenzyme (protein) and its cofactors forms a holoenzyme. Cofactors can be inorganic ions or organic coenzymes.

Apoenzyme: Protein portion, inactive without cofactors.
Cofactor: Nonprotein component (inorganic or organic).
Coenzyme: Organic cofactor, often derived from vitamins.
Holoenzyme: Active enzyme with all necessary cofactors.

Diagram of holoenzyme structure

Representative Cofactors of Enzymes

Cofactors are essential for enzyme function, facilitating various biochemical transformations. They may be metal ions or organic molecules (coenzymes).

Cofactor	Example of Use	Substance Transferred	Vitamin Source
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 Krebs cycle	Acetyl group	Pantothenic acid (B5)
Pyridoxal phosphate	Transamination in the synthesis of amino acids	Amino group (–NH2)	Pyridoxine (B6)
Thiamine pyrophosphate	Decarboxylation of pyruvic acid	Aldehyde group (–CHO)	Thiamine (B1)

Table of representative cofactors of enzymes

Activation Energy and Enzyme Activity

Enzymes lower the activation energy required for chemical reactions, thereby increasing the rate of reaction. The active site of an enzyme binds to the substrate, facilitating the transformation.

Activation Energy: Minimum energy required to initiate a reaction.
Active Site: Region of enzyme where substrate binds.
Substrate: Molecule upon which an enzyme acts.

Graph showing effect of enzymes on activation energy

Enzyme-Substrate Interaction

Enzymes exhibit specificity for their substrates, often described by the induced fit model. Substrate binding induces a conformational change in the enzyme's active site.

Induced Fit Model: Active site changes shape to fit substrate.

Diagram of enzyme-substrate induced fit

Factors Affecting Enzyme Activity

Enzyme activity is influenced by temperature, pH, substrate concentration, and the presence of inhibitors. Each factor can alter the rate and efficiency of enzymatic reactions.

Temperature: Optimal range enhances activity; extremes cause denaturation.
pH: Each enzyme has an optimal pH; deviations can denature proteins.
Substrate Concentration: Increased concentration raises activity until saturation is reached.
Inhibitors: Competitive and noncompetitive inhibitors reduce enzyme activity.

Graph of enzyme activity vs temperature Diagram of functional and denatured protein Graph of enzyme activity vs pH Graph of enzyme activity vs substrate concentration

Control of Enzymatic Activity

Enzyme activity can be regulated by activators and inhibitors. Allosteric activation and inhibition are key mechanisms, as is feedback inhibition, which controls metabolic pathways.

Allosteric Activation: Activator binds to allosteric site, enabling active site function.
Competitive Inhibition: Inhibitor competes with substrate for active site.
Noncompetitive Inhibition: Inhibitor binds to allosteric site, distorting active site.
Feedback Inhibition: End-product inhibits pathway, preventing overproduction.

Diagram of allosteric activation Diagram of competitive inhibition Diagram of noncompetitive inhibition Diagram of feedback inhibition

Carbohydrate Catabolism

Glucose Catabolism: Respiration and Fermentation

Glucose is the primary carbohydrate used by most organisms for energy. It is catabolized by cellular respiration or fermentation, depending on the availability of oxygen.

Cellular Respiration: Complete oxidation of glucose to CO2 and H2O, producing ATP.
Fermentation: Partial oxidation of glucose, producing less ATP and various end-products.

Summary diagram of glucose catabolism

Glycolysis

Glycolysis occurs in the cytoplasm and splits glucose into two molecules of pyruvic acid. It consists of three stages: energy-investment, lysis, and energy-conserving.

Net Gain: 2 ATP, 2 NADH, and 2 pyruvic acid per glucose.
Substrate-level phosphorylation: Direct transfer of phosphate to ADP.

Diagram of glycolysis stages Diagram of substrate-level phosphorylation

Cellular Respiration: Synthesis of Acetyl-CoA

Pyruvic acid is converted to acetyl-CoA, which enters the Krebs cycle. This process produces NADH and CO2.

Products: 2 acetyl-CoA, 2 NADH, 2 CO2 per glucose.

Diagram of pyruvate dehydrogenase complex

Krebs Cycle

The Krebs cycle occurs in the cytosol of prokaryotes and mitochondrial matrix of eukaryotes. It transfers energy to NAD+ and FAD, producing ATP, NADH, FADH2, and CO2.

Products: 2 ATP, 2 FADH2, 6 NADH, 4 CO2 per glucose.

Diagram of Krebs cycle

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 used for ATP synthesis via chemiosmosis.

Aerobic Respiration: Oxygen is the final electron acceptor.
Anaerobic Respiration: Other molecules (e.g., NO3-, SO42-) serve as acceptors.
ATP Yield: Up to 34 ATP per glucose via oxidative phosphorylation.

Diagram of electron transport chain in prokaryotes Table of ATP yield in prokaryotic aerobic respiration

Metabolic Diversity: Alternative Pathways

Bacteria may use alternative pathways for glucose catabolism, such as the Entner-Doudoroff and pentose phosphate pathways. These pathways produce different amounts of ATP and precursor metabolites.

Entner-Doudoroff Pathway: Found only in prokaryotes; produces 1 ATP, 1 NADH, 1 NADPH.
Pentose Phosphate Pathway: Produces NADPH and precursor metabolites for biosynthesis.

Fermentation

Fermentation provides cells with an alternative source of NAD+ when oxygen is unavailable. It results in the production of various end-products, which can be used to identify bacteria.

End-products: Lactic acid, ethanol, propionic acid, acetone, etc.
Biochemical Tests: Used to identify bacteria based on fermentation products.

Diagram of fermentation pathways Diagram of fermentation products and representative microbes

Other Catabolic Pathways

Lipid Catabolism

Lipids are hydrolyzed into glycerol and fatty acids. Glycerol enters glycolysis, while fatty acids undergo beta-oxidation to produce acetyl-CoA, NADH, and FADH2.

Hydrolysis: Lipase separates fatty acids from glycerol.
Beta-oxidation: Sequential removal of two-carbon units from fatty acids.

Diagram of lipid hydrolysis Diagram of beta-oxidation of fatty acids

Protein Catabolism

Proteins are broken down into amino acids, which are deaminated to remove the amino group. The resulting carbon skeletons enter the citric acid cycle for energy production.

Deamination: Removal of amino group, producing ammonia and other nitrogenous wastes.

Diagram of protein catabolism and deamination

Photosynthesis

Photosynthetic Structures and Reactions

Photosynthetic organisms capture light energy using chlorophyll and photosystems embedded in thylakoid membranes. Photosynthesis consists of light-dependent and light-independent reactions.

Light-dependent reactions: Use light energy to produce ATP and NADPH.
Light-independent reactions: Use ATP and NADPH to fix CO2 into glucose (Calvin-Benson cycle).

Diagram of photosystem and chlorophyll structure

Integration and Regulation of Metabolic Function

Regulation of Metabolic Pathways

Cells regulate metabolism by controlling enzyme synthesis and activity. Feedback inhibition, compartmentalization, and gene expression are key regulatory mechanisms.

Feedback Inhibition: Prevents overproduction of end-products.
Compartmentalization: Eukaryotes isolate pathways in organelles.
Gene Expression: Controls timing and amount of enzyme production.
Metabolic Expression: Controls activity of enzymes once produced.

Additional info: Regulation ensures efficient use of resources and prevents wasteful overproduction of metabolites.