Microbial Metabolism, Nutrition, Growth, and Genetics: Study Guide (Chapters 5-7)

Microbial Metabolism

Catabolism vs. Anabolism

Metabolism encompasses all chemical reactions within a cell, divided into catabolic (breakdown) and anabolic (synthesis) pathways. These processes are interconnected, with catabolism providing energy and building blocks for anabolism.

• Catabolism: Breakdown of complex molecules into simpler ones, releasing energy (exergonic). ("demolition crew" break things)

• Anabolism: Synthesis of complex molecules from simpler ones, requiring energy (endergonic).(add together or build muscle ATP gets used.)

• Amphibolic reactions: Pathways that serve both catabolic and anabolic functions, e.g., citric acid cycle. ("2 way street" like Krebs Cycle switches on body needs)

• Biomolecules: Include carbohydrates(Sugars/energy), lipids(stored energy), proteins(machinery/muscle), and nucleic acids(Instruction Manual DNA,RNA,ATP); catabolism and anabolism involve their interconversion. ("building bricks of life.")

• Link: ATP and reducing power (NADH, FADH2) connect catabolic and anabolic reactions.

Key Definitions

• Metabolism: All chemical reactions in a cell.

• Catabolism: Energy-releasing breakdown reactions.

• Anabolism: Energy-consuming synthesis reactions.

• Endergonic: Reactions that absorb energy.

• Exergonic: Reactions that release energy.

ATP: Structure and Function

ATP (adenosine triphosphate) is the primary energy carrier in cells.

• Structure: Adenine base, ribose sugar, three phosphate groups.

• Function: Stores and transfers energy for cellular processes.

• Hydrolysis: ATP → ADP + Pi releases energy.

Enzymes: Structure, Function, and Regulation

Enzymes are biological catalysts that speed up reactions by lowering activation energy.

• Structure: Protein (sometimes with cofactors/coenzymes).

• Function: Specific for substrates; catalyze reactions efficiently.

• Conditions affecting function: Temperature, pH, substrate concentration.

• Denaturation: Loss of enzyme structure and function due to extreme conditions.

• Activation energy: Minimum energy required to start a reaction.

Enzyme Inhibition

• Allosteric inhibition: Inhibitor binds to site other than active site, changing enzyme shape.

• Competitive inhibition: Inhibitor competes with substrate for active site.

• Noncompetitive inhibition: Inhibitor binds elsewhere, reducing enzyme activity.

• Feedback inhibition: End product inhibits pathway, maintaining homeostasis.

• Sulfanilamide: Acts as a competitive inhibitor, blocking folic acid synthesis in bacteria.

Oxidation-Reduction (Redox) Reactions

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Coenzymes: NAD+, FAD, NADP+ shuttle electrons during metabolism.

Carbohydrate Catabolism Pathways

Cells extract energy from carbohydrates via sequential pathways.

1. Glycolysis: Occurs in cytoplasm; converts glucose to pyruvate, produces ATP and NADH.

2. Acetyl-CoA synthesis: Pyruvate converted to acetyl-CoA, produces NADH and CO2.

3. Citric Acid Cycle (Krebs): Acetyl-CoA oxidized, produces NADH, FADH2, ATP, CO2.

4. Electron Transport Chain (ETC): Located in plasma membrane (prokaryotes) or mitochondria (eukaryotes); uses NADH/FADH2 to generate ATP via chemiosmosis.

• Proton movement during chemiosmosis: Drives ATP synthesis by ATP synthase.

Fermentation

• Purpose: Replenishes NAD+ for glycolysis when oxygen is absent.

• Types: Alcoholic (produces ethanol), lactic acid (produces lactate).

Catabolism of Fats and Proteins

• Fats: Broken down by beta-oxidation to acetyl-CoA.

• Proteins: Deaminated to enter catabolic pathways.

• Central Catabolism: Carbohydrate catabolism is central as other macromolecules feed into these pathways.

Phosphorylation Mechanisms

• Oxidative phosphorylation: ATP generated via ETC and chemiosmosis.

• Substrate-level phosphorylation: ATP generated directly in metabolic pathways (e.g., glycolysis).

Regulation of Metabolism

• Cells regulate metabolism via enzyme activity, gene expression, and feedback inhibition.

Microbial Nutrition and Growth

Oxygen Requirements and Energy Metabolism

Microbes are classified by their oxygen requirements, which influence their energy metabolism and protective mechanisms against toxic oxygen.

• Obligate aerobe: Requires oxygen; uses aerobic respiration.

• Obligate anaerobe: Cannot tolerate oxygen; uses anaerobic respiration or fermentation.

• Facultative anaerobe: Can grow with or without oxygen; uses both aerobic and anaerobic pathways.

• Aerotolerant anaerobe: Tolerates oxygen but does not use it for metabolism.

• Microaerophile: Requires low oxygen concentrations.

• FTM (Fluid Thioglycolate Media): Used to distinguish oxygen requirements in lab.

Binary Fission

• Process: Prokaryotic cell division; cell duplicates DNA, elongates, and splits into two identical cells.

• Difference from mitosis: Binary fission is simpler, lacks mitotic spindle.

• Result: Two genetically identical daughter cells.

Nutritional Requirements for Growth

• Microbes require carbon, nitrogen, sulfur, phosphorus, trace elements, and growth factors.

• These nutrients are used for biosynthesis and energy production.

Phases of Microbial Growth

• Lag phase: Cells adapt, no division.

• Log (exponential) phase: Rapid cell division.

• Stationary phase: Growth rate slows, nutrients deplete.

• Death phase: Cells die off.

• Lab relevance: Gram stain results and antibiotic sensitivity depend on growth phase.

Trophic Classification of Microbes

• Chemoheterotrophs: Use organic compounds for energy and carbon.

• Photoautotrophs: Use light for energy, CO2 for carbon.

• Chemoautotrophs: Use inorganic compounds for energy, CO2 for carbon.

• Photoheterotrophs: Use light for energy, organic compounds for carbon.

Environmental Effects on Growth

• Temperature: Human pathogens are mesophiles (grow best at 20-40°C).

• pH: Most pathogens prefer neutral pH.

• Osmotic pressure: Pathogens require isotonic environments.

Bacterial Population Growth

• Exponential (logarithmic) growth: Population doubles each generation.

• Arithmetic growth: Linear increase.

• Calculation: $N = N_0 \times 2^n$ where $N_0$ is initial cell number, $n$ is generations.

Toxic Forms of Oxygen and Protective Enzymes

Toxic Oxygen Form	Protective Enzyme
Singlet oxygen	Carotenoids
Superoxide radical	Superoxide dismutase
Peroxide anion	Catalase, peroxidase
Hydroxyl radical	No specific enzyme; minimized by other mechanisms

Biofilms and Quorum Sensing

• Biofilms: Communities of microbes attached to surfaces, embedded in extracellular matrix.

• Clinical importance: Resistant to antibiotics, cause persistent infections.

• Quorum sensing: Cell-to-cell communication regulating gene expression in response to population density.

Culturing Bacteria

• Defined media: Exact chemical composition known.

• Complex media: Contains unknown components (e.g., extracts).

• Differential media: Distinguishes between organisms based on biochemical reactions.

• Selective media: Favors growth of specific microbes.

Pure Culture Techniques

• Streak plate: Isolates colonies.

• Pour plate: Quantifies colonies.

• Colony forming unit (CFU): Single cell or group giving rise to a colony.

• Axenic culture: Pure culture of one species.

• Aseptic technique: Prevents contamination.

Cell Counting Methods

• CFU count: Plate count method.

• Turbidity measurement: Uses spectrophotometer to estimate cell density.

• Viable count: Number of living cells.

Microbial Genetics

Ames Test and Auxotrophs

• Ames test: Detects mutagenic potential of chemicals by measuring mutation rate in bacteria.

• Auxotroph: Mutant organism lacking ability to synthesize a particular nutrient.

• Limitations: Ames test does not indicate carcinogenicity in humans directly.

Mutations

• Point mutations: Affect single nucleotide.

• Silent: No change in protein.

• Missense: Changes one amino acid.

• Nonsense: Introduces stop codon.

• Frameshift: Insertion/deletion alters reading frame.

Nucleotide Structure and Genetic Code

• Nucleotide: 5-carbon sugar, phosphate, nitrogenous base.

• DNA vs. RNA: DNA has deoxyribose, thymine; RNA has ribose, uracil.

• Genetic code: Specifies amino acids via codons.

• Types of RNA: mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

Replication, Transcription, Translation

• Replication: DNA copied by DNA polymerase; semiconservative (each new DNA has one old strand).

• Transcription: DNA → RNA by RNA polymerase.

• Translation: mRNA decoded by ribosome to synthesize protein.

• Enzymes: DNA polymerase, RNA polymerase, ribosome.

• Substrates: Nucleotides, amino acids.

Mutagens

• Mutagen: Agent causing mutations (e.g., chemicals, radiation).

• Results: Can cause silent, missense, nonsense, or frameshift mutations.

Horizontal Gene Transfer

• Transformation: Uptake of naked DNA from environment.

• Transduction: Transfer via bacteriophage; can be specialized or general.

• Conjugation: Transfer via direct cell contact, often using pilus.

• Bacterial pilus: Facilitates DNA transfer during conjugation.

Chromosomes and Plasmids

• Prokaryotic chromosomes: Usually single, circular DNA.

• Eukaryotic chromosomes: Multiple, linear DNA.

• Plasmids: Small, circular DNA molecules; can carry antibiotic resistance genes.

• F plasmid: Fertility plasmid involved in conjugation.

Genetic Recombination

• Occurs during horizontal gene transfer or sexual reproduction; results in new genetic combinations.

Proofreading Error Rates

• DNA polymerase: Low error rate due to proofreading.

• RNA polymerase: Higher error rate; lacks proofreading.

Operons: Inducible vs. Repressible

• Inducible operon: Usually off; turned on by substrate (e.g., lac operon).

• Repressible operon: Usually on; turned off by end product (e.g., trp operon).

• Promoter: DNA sequence where RNA polymerase binds to start transcription.

Lactose (lac) Operon

• Structure: Includes promoter, operator, structural genes.

• Function: Controls expression of genes for lactose metabolism.

• Regulation: Induced by lactose; repressed when glucose is present.

• Homeostasis: Ensures efficient use of energy sources.