Microbial Metabolism, Catabolism, Anabolism, and Genetic Regulation

CHAPTER 10: METABOLISM

Overview of Metabolism

Metabolism encompasses all chemical reactions occurring within a cell, including both energy-producing and energy-consuming processes. These reactions are essential for cellular function and survival.

• Redox Reactions: Involve oxidation (loss of electrons) and reduction (gain of electrons).

• Electron Transport Chain (ETC): Central to ATP production via oxidative phosphorylation.

• Types of Cellular Work:

  • Chemical work: Synthesis of molecules.

  • Transport work: Movement of substances across membranes.

  • Mechanical work: Cellular movement (e.g., flagella, cytoplasmic streaming).

• ATP: The universal energy currency, composed of adenine, ribose, and three phosphate groups.

Thermodynamics in Metabolism

Cellular reactions obey the laws of thermodynamics, which govern energy transformations.

• First Law: Energy cannot be created or destroyed.

• Second Law: Energy transfers increase entropy (disorder).

• Free Energy (ΔG): Determines spontaneity of reactions.

  • $\Delta G = \Delta H - T\Delta S$

  • $\Delta G < 0$ : Exergonic (spontaneous)

  • $\Delta G > 0$ : Endergonic (non-spontaneous)

• Standard Free Energy (ΔG°′): Indicates spontaneity under standard conditions.

Redox Reactions and Electron Flow

• Reduction Potential (E₀′): Measures tendency to gain/lose electrons.

  • More negative E₀′: Better electron donor.

  • More positive E₀′: Better electron acceptor.

  • Electrons flow from negative to positive E₀′.

Electron Transport Chain (ETC)

The ETC is a series of electron carriers that transfer electrons, release energy, and synthesize ATP.

• Location: Plasma membrane (prokaryotes), mitochondria/chloroplasts (eukaryotes).

• Carriers: NAD⁺/NADP⁺, FAD/FMN, Coenzyme Q, cytochromes, iron-sulfur proteins.

Biochemical Pathways

• Linear: Direct progression from start to end.

• Cyclic: Repeats (e.g., TCA cycle).

• Branched: Multiple products.

Enzymes and Regulation

Enzymes are protein catalysts that speed up reactions without being consumed.

• Structure: Apoenzyme (protein), cofactor (helper), holoenzyme (active form).

• Activity depends on: Substrate concentration, pH, temperature.

• Regulation:

  • Competitive inhibition: Competes for active site.

  • Noncompetitive inhibition: Binds elsewhere.

  • Allosteric regulation: Positive/negative effectors.

  • Covalent modification: Adds/removes groups (e.g., phosphate).

  • Feedback inhibition: End product inhibits pathway.

Ribozymes and Metabolic Regulation

• Ribozymes: RNA molecules acting as enzymes (e.g., self-splicing RNA).

• Regulation Mechanisms:

  • Metabolic channeling: Organizes enzymes spatially.

  • Gene regulation: Controls enzyme synthesis.

  • Enzyme activity control: Modifies enzyme function.

CHAPTER 11: CATABOLISM

Catabolic Processes

Catabolism involves breaking down complex molecules to simpler ones, generating ATP, NADH, and building blocks for biosynthesis.

• Sources:

  • Carbon: Autotrophs (CO₂), heterotrophs (organic carbon).

  • Energy: Phototrophs (light), chemotrophs (chemicals).

  • Electrons: Lithotrophs (inorganic), organotrophs (organic).

• Nutritional Types:

  • Photolithoautotroph: Light, CO₂, inorganic electron donor.

  • Photoorganoheterotroph: Light, organic carbon, organic electron donor.

  • Chemolithoautotroph: Inorganic electron donor, CO₂.

  • Chemolithoheterotroph: Inorganic electron donor, organic carbon.

  • Chemoorganoheterotroph: Organic electron donor, organic carbon (most pathogens).

Fueling Reactions

• Respiration: Uses ETC; aerobic (O₂ as final acceptor), anaerobic (other acceptors). Produces most ATP.

• Fermentation: No ETC; uses organic molecules as acceptor. Produces less ATP.

Glycolysis and TCA Cycle

• Glycolysis: Glucose is converted to 2 pyruvate.

• TCA Cycle: Per acetyl-CoA: 3 NADH, 1 FADH₂, 1 GTP (ATP), 2 CO₂.

ETC and ATP Production

• Oxidative Phosphorylation: Most ATP produced.

• Chemiosmosis: ETC pumps H⁺ out, creating proton motive force (PMF).

• ATP Synthase: H⁺ flows back in to make ATP.

• ATP Yield: 32 ATP per glucose in eukaryotes.

Anaerobic Respiration and Fermentation

• Anaerobic Respiration: Uses ETC, final acceptor not O₂. Less ATP than aerobic.

• Fermentation: No ETC, regenerates NAD⁺, ATP from substrate-level phosphorylation.

  • Lactic acid: Produces lactate.

  • Alcoholic: Produces ethanol and CO₂.

  • Mixed acid: Produces multiple acids.

  • Butanediol: Produces butanediol.

Catabolism of Other Molecules

• Carbohydrates: Converted to glycolysis intermediates.

• Lipids: Glycerol enters glycolysis; fatty acids undergo beta oxidation to acetyl-CoA.

• Proteins: Deamination removes NH₂ group.

Photosynthesis

• Light Reactions: Produce ATP and NADPH.

• Dark Reactions: Convert CO₂ to organic molecules.

• Oxygenic: Produces O₂, electron source is H₂O.

• Anoxygenic: Does not produce O₂, electron source is H₂S.

• Cyclic: Produces ATP only.

• Noncyclic: Produces ATP and NADPH.

• Rhodopsin Phototrophy: Light pumps H⁺ to PMF, no ETC.

CHAPTER 12: ANABOLISM

Anabolic Processes

Anabolism uses energy from catabolism to build complex molecules via biosynthetic pathways.

• Principles:

  • Builds from small to large molecules (monomers to macromolecules).

  • Many enzymes function in both directions.

• Cofactors: Catabolism uses NADH; anabolism uses NADPH.

Calvin-Benson Cycle

The Calvin-Benson cycle is the primary pathway for carbon fixation in photoautotrophs.

• Carboxylation Phase: CO₂ + RuBP forms 3-PGA (enzyme: RuBisCO).

• Reduction Phase: 3-PGA is reduced to G3P using ATP and NADPH.

• Regeneration Phase: Reforms RuBP.

• Per CO₂: 3 ATP + 2 NADPH used.

Precursor Metabolites and Biosynthesis

• Precursor Metabolites: Small molecules from glycolysis and TCA cycle used to build amino acids, nucleotides, sugars.

• Carbohydrate Synthesis: Gluconeogenesis makes glucose from non-carbohydrates; uses many glycolysis enzymes and three unique bypass steps.

  • UDP-glucose used for sugar synthesis.

  • ATP and UTP required.

• Peptidoglycan Synthesis: Uses UDP derivatives and bactoprenol; cross-linking via transpeptidation (antibiotics target this step).

Amino Acid, Nucleotide, and Lipid Synthesis

• Amino Acids: Built from carbon skeleton + NH₃ (+ sometimes S).

  • Nitrogen assimilation: Sources are ammonia and nitrate; fixation uses nitrogenase (requires ATP).

  • Sulfur assimilation: Source is sulfate; converted to cysteine.

• Nucleotide Synthesis:

  • Purines: Two rings (A, G), built on ribose.

  • Pyrimidines: One ring (C, T, U), ring formed first then attached.

  • Nucleoside: Base + sugar; nucleotide: nucleoside + phosphate.

• Lipids:

  • Fatty acids made from acetyl-CoA + malonyl-CoA (uses NADPH and ACP).

  • Saturated (no double bonds), unsaturated (double bonds).

  • Major lipids: Triacylglycerols (storage), phospholipids (membranes), sterols (eukaryotes), isoprenoids (archaea).

  • LPS: Gram-negative bacteria (Lipid A + core + O-antigen).

CHAPTER 13: BACTERIAL GENOME REPLICATION AND EXPRESSION

Discovery of Genetic Material

• Frederick Griffith: Demonstrated transformation in bacteria.

• Oswald Avery: Proved DNA is genetic material.

• Hershey and Chase: Confirmed DNA carries genetic information.

DNA, RNA, and Protein Structure

• DNA: Double-stranded, deoxyribose, bases A, T, G, C.

• RNA: Single-stranded, ribose, bases A, U, G, C.

• Base Pairing: A-T (2 bonds), G-C (3 bonds).

• Protein Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helix/beta sheet.

  • Tertiary: 3D shape.

  • Quaternary: Multiple chains.

DNA Replication

• Semiconservative: One old and one new strand.

• Bidirectional: From one origin.

• Key Enzymes:

  • Helicase: Unwinds DNA.

  • SSB: Stabilizes strands.

  • Primase: Makes RNA primer.

  • DNA polymerase: Synthesizes DNA (5’ to 3’).

  • Ligase: Joins fragments.

• Leading Strand: Continuous synthesis.

• Lagging Strand: Okazaki fragments.

Gene Structure and Expression

• Promoter: RNA polymerase binding site.

• Leader: Not translated.

• Coding Region: Encodes protein.

• Start Codon: AUG.

• Stop Codons: UAA, UAG, UGA.

Transcription and Translation

• Transcription: DNA to RNA (enzyme: RNA polymerase).

  • Initiation: Sigma factor binds promoter.

  • Elongation: RNA synthesized 5’ to 3’.

  • Termination: Rho-dependent or independent.

  • Operon: Multiple genes under one promoter.

• Genetic Code: Codon (3 bases) specifies 1 amino acid; degenerate (multiple codons per amino acid).

• Translation: mRNA to protein at ribosome.

  • tRNA: Carries amino acids (anticodon matches codon).

  • Ribosome sites: A (entry), P (growing chain), E (exit).

  • Initiation, elongation, termination.

  • First amino acid: fMet (bacteria).

• Secretion Systems: Move proteins out of cell.

CHAPTER 14: REGULATION OF CELLULAR PROCESSES

Gene Regulation

Cells regulate gene expression to adapt to environmental changes and conserve resources.

• Constitutive Genes: Always ON.

• Regulated Genes: Turned ON/OFF as needed.

• Inducible Genes: Turned ON by inducer (e.g., lactose metabolism).

• Repressible Genes: Turned OFF by corepressor (e.g., amino acid synthesis).

Transcriptional Control

• Negative Control: Repressor blocks RNA polymerase.

• Positive Control: Activator helps RNA polymerase bind.

• Operon: Group of genes controlled together.

Lac, Trp, and Ara Operons

• Lac Operon: Controls lactose metabolism.

  • No lactose: Repressor binds, transcription OFF.

  • Lactose present: Allolactose binds repressor, transcription ON.

  • Glucose present: Low cAMP, CAP inactive, transcription LOW.

  • Low glucose: High cAMP, CAP active, transcription HIGH.

• Trp Operon: Controls tryptophan synthesis.

  • No tryptophan: Operon ON.

  • Tryptophan present: Acts as corepressor, operon OFF.

• Ara Operon: Positive and negative control by AraC protein depending on arabinose presence.

Translation Regulation and Global Control

• Riboswitches: mRNA changes shape to block ribosome binding.

• RNA Thermometers: Temperature changes RNA structure, affecting translation.

• Small RNAs (sRNA): Bind mRNA to inhibit/enhance translation.

• Global Regulation: Controls many genes at once (regulon).

  • Two-component system: Sensor kinase and response regulator.

  • Phosphorelay: Multi-step signaling pathway.

  • Sigma factors: Direct RNA polymerase to specific genes.

  • Second messengers: cAMP, ppGpp, c-di-GMP.

Other Regulatory Mechanisms

• Chemotaxis: Movement toward/away from stimuli (MCP, CheA, CheY proteins).

• Quorum Sensing: Cell communication for virulence, biofilm production.

• Sporulation: Triggered by starvation, controlled by sigma factors and phosphorelay (Spo0A regulator).

• Defense Systems: Restriction-modification (cuts foreign DNA), CRISPR-Cas (adaptive immunity).

Summary Table: Metabolic Pathways and Regulation

Pathway	Main Function	Key Products	Regulation
Glycolysis	Glucose breakdown	ATP, NADH, pyruvate	Feedback inhibition
TCA Cycle	Energy production, biosynthesis	NADH, FADH₂, GTP, CO₂	Allosteric regulation
ETC	ATP synthesis	ATP, H₂O	Substrate availability
Calvin Cycle	Carbon fixation	G3P, RuBP	Enzyme activity
Lac Operon	Lactose metabolism	Enzymes for lactose use	Inducer (allolactose), CAP/cAMP
Trp Operon	Tryptophan synthesis	Tryptophan	Corepressor (tryptophan), attenuation

Additional info: Academic context was added to clarify pathway functions, regulatory mechanisms, and enzyme roles for completeness.