Microbial Metabolism: Study Guide and Key Concepts

Microbial Metabolism

Overview of Metabolism

Microbial metabolism encompasses all controlled biochemical reactions that occur within cells, enabling organisms to obtain energy, build cellular structures, and regulate their internal environment. Metabolism is divided into two main processes: catabolism and anabolism.

• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy. These reactions are exergonic (energy-releasing).

• Anabolism: The synthesis of complex molecules from simpler precursors, requiring energy input. These reactions are endergonic (energy-consuming).

• Energy Storage: Energy released from catabolic reactions is stored in the form of adenosine triphosphate (ATP).

• Decarboxylation: The removal of a CO2 group from a molecule, often seen in metabolic pathways.

ATP: The Energy Currency of the Cell

ATP is the primary molecule used by cells to store and transfer energy. Energy is stored in the high-energy phosphate bonds of ATP, which can be released by hydrolysis to ADP and inorganic phosphate.

• ATP Structure: Consists of adenine, ribose, and three phosphate groups.

• ATP Hydrolysis: $\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P_i}$

• ATP Synthesis: Occurs via phosphorylation of ADP.

Electron Carriers in Metabolism

Electron carriers are molecules that transport electrons during metabolic reactions, often as hydrogen atoms. They play a crucial role in redox reactions and energy production.

• NAD+ / NADH: Nicotinamide adenine dinucleotide; involved in catabolic reactions.

• NADP+ / NADPH: Nicotinamide adenine dinucleotide phosphate; involved in anabolic reactions.

• FAD / FADH2: Flavine adenine dinucleotide; participates in the Krebs cycle and electron transport chain.

Phosphorylation Mechanisms

Phosphorylation is the process of adding a phosphate group to ADP to form ATP. There are three main types:

• Substrate-level phosphorylation: Direct transfer of a phosphate group from a substrate to ADP. Occurs in glycolysis and the Krebs cycle.

• Oxidative phosphorylation: ATP is generated using energy from the electron transport chain and chemiosmosis.

• Photophosphorylation: ATP is produced using light energy during photosynthesis (less relevant for most bacteria).

Biological Molecules: Proteins and Amino Acids

Proteins are essential macromolecules with diverse functions, including catalysis, regulation, transport, and defense. They are sensitive to environmental conditions such as pH, temperature, and ionic concentration.

• Monomer: Amino acids (21 types).

• Polymer: Proteins, formed by peptide bonds (covalent).

• Structure: Determined by amino acid sequence and side groups.

• Function: Enzymes, structural support, regulation, transport, immune defense.

Enzymes in Metabolism

Enzymes are biological catalysts that accelerate chemical reactions by lowering activation energy. Most enzymes are proteins, and some require cofactors for activity.

• Active Site: Region where substrate binds and reaction occurs.

• Induced-fit Model: Enzyme changes shape to accommodate substrate.

• Enzyme Activity: Influenced by temperature, pH, ionic concentration, enzyme and substrate concentrations, and inhibitors.

• Denaturation: Extreme changes in temperature, pH, or ionic concentration can permanently inactivate enzymes.

Enzyme Inhibition

Enzyme inhibitors are molecules that decrease enzyme activity by preventing substrate binding.

• Competitive Inhibitors: Bind to the active site, blocking substrate access. Example: Sulfanilamide (antibiotic).

• Noncompetitive Inhibitors: Bind to an allosteric site, changing enzyme shape and reducing activity.

• Examples: Penicillin, Aspirin, Lipitor.

Carbohydrate Catabolism

Most organisms use carbohydrates, especially glucose, as their primary energy source. Glucose catabolism occurs via two main pathways: cellular respiration and fermentation.

• Cellular Respiration: Complete breakdown of glucose to CO2 and H2O. Involves glycolysis, Krebs cycle, and electron transport chain.

• Fermentation: Partial oxidation of glucose, converting pyruvate to organic products (e.g., lactate, ethanol, acetate).

Glycolysis

Glycolysis is the first step in glucose catabolism, occurring in the cytoplasm of all cells. It splits glucose (6 carbons) into two pyruvate molecules (3 carbons each).

• Net ATP Gain: 2 ATP (via substrate-level phosphorylation).

• Products: 2 pyruvate, 2 NADH, 2 ATP.

• Some electrons: Carried to the electron transport chain for further ATP production.

Cellular Respiration

Cellular respiration is the complete oxidation of pyruvate to CO2 and H2O, producing ATP through a series of redox reactions.

• Stages: Conversion of pyruvate to acetyl-CoA, Krebs cycle, electron transport chain.

• Location: Cytosol in prokaryotes; mitochondrial matrix in eukaryotes.

• ATP Yield: Up to 38 ATP per glucose in prokaryotes.

Krebs Cycle

• Acetyl-CoA: Formed from pyruvate; enters the cycle.

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

• Energy Transfer: Most energy is transferred to NAD+ and FAD.

Electron Transport Chain (ETC)

• Location: Inner mitochondrial membrane (eukaryotes), cytoplasmic membrane (prokaryotes).

• Function: Transfers electrons from NADH and FADH2 through a series of carriers, generating a proton gradient.

• Final Electron Acceptors: O2 (aerobic), other molecules (anaerobic: SO42-, NO3-, CO32-).

• ATP Synthase: Uses proton motive force to synthesize ATP (oxidative phosphorylation).

Fermentation

Fermentation is an alternative pathway for energy production when cells lack an electron transport chain or oxygen. It regenerates NAD+ for glycolysis by reducing organic molecules.

• ATP Yield: Lower than respiration; only substrate-level phosphorylation occurs.

• Products: Lactate, ethanol, acetate (varies by organism).

• Commercial Products: Alcohol, yogurt, cheese, vinegar.

Integration and Regulation of Metabolism

Cells regulate metabolic pathways to optimize energy use and respond to environmental changes.

• Catabolic Enzymes: Synthesized only when substrate is available.

• Energy Source Preference: Cells use the most energy-efficient substrate first.

• Anabolic Reactions: Synthesis occurs only if the molecule is not available externally.

• Amphibolic Reactions: Pathways that function in both catabolism and anabolism.

Key Vocabulary

• Metabolism: All chemical reactions in a cell.

• Catabolism: Breakdown of molecules.

• Anabolism: Synthesis of molecules.

• Reduction: Gain of electrons.

• Oxidation: Loss of electrons.

• ATP: Energy currency.

• Electron Carriers: NAD+, NADH, FAD, FADH2.

• Enzyme: Biological catalyst.

• Substrate: Molecule acted upon by an enzyme.

• Activation Energy: Energy required to start a reaction.

• Induced-fit Model: Enzyme changes shape for substrate.

• Active Site: Enzyme region for substrate binding.

• Allosteric Site: Regulatory site on enzyme.

• Competitive Inhibitor: Blocks active site.

• Noncompetitive Inhibitor: Alters enzyme shape.

• Ribozyme: RNA enzyme.

• Cellular Respiration: Complete oxidation of glucose.

• Oxidative Phosphorylation: ATP synthesis via ETC.

• Substrate-level Phosphorylation: Direct ATP synthesis.

• Photophosphorylation: ATP synthesis using light.

• Fermentation: Partial oxidation of glucose.

• Aerobic: Uses O2 as final electron acceptor.

• Anaerobic: Uses other molecules as final electron acceptor.

• Glycolysis: Glucose breakdown.

• Krebs Cycle: Acetyl-CoA oxidation.

• Electron Transport: Electron transfer for ATP.

• ATPase: Enzyme for ATP synthesis.

• Chemiosmosis: Movement of ions for ATP production.

• Photosynthesis: Light-driven synthesis.

• Lipid Catabolism: Beta-oxidation.

• Protein Catabolism: Deamination.

• Biosynthesis: Anabolic pathways.

Comparison Table: Aerobic Respiration, Anaerobic Respiration, Fermentation

Pathway	Final Electron Acceptor	ATP Yield (per glucose)	Key Products
Aerobic Respiration	O2	~38	CO2, H2O
Anaerobic Respiration	SO42-, NO3-, CO32-	Variable (<38)	CO2, H2O, other products
Fermentation	Organic molecules	2	Lactate, ethanol, acetate

Scientific Contribution: Peter Mitchell

Peter Mitchell proposed the chemiosmotic theory, explaining how ATP is synthesized by the movement of protons across a membrane, driven by the electron transport chain. This process is fundamental to oxidative phosphorylation.

Example Applications

• Fermentation: Used in production of alcohol, yogurt, cheese, and vinegar.

• Enzyme Inhibitors: Antibiotics (e.g., sulfanilamide), drugs (e.g., aspirin, Lipitor).

Additional info: Amphibolic reactions are pathways that serve both catabolic and anabolic functions, such as glycolysis and the Krebs cycle. Regulation of metabolism ensures efficient use of resources and adaptation to environmental changes.