Metabolism

Gibbs Free Energy and Enzyme Catalysis

Metabolism involves chemical reactions that are catalyzed by enzymes, affecting the energy profile of reactants and products. Gibbs free energy graphs illustrate these changes.

• Gibbs Free Energy (ΔG): Represents the energy difference between reactants and products. Negative ΔG indicates a spontaneous reaction.

• Activation Energy: The energy required to initiate a reaction. Enzymes lower activation energy, increasing reaction speed, but do not alter ΔG.

• Enzyme Catalysis: Enzymes accelerate reactions by stabilizing the transition state.

• Substrate: The molecule upon which an enzyme acts, binding at the enzyme's active site.

• Cofactors vs. Coenzymes: Cofactors are inorganic (e.g., metal ions), while coenzymes are organic molecules (e.g., NAD+). An apoenzyme is the protein part alone; a holoenzyme is the complete, active enzyme with its cofactor/coenzyme.

• Competitive vs. Non-Competitive Inhibitors: Competitive inhibitors bind the active site; non-competitive inhibitors bind the allosteric site, altering enzyme activity.

• Allosteric Site: A regulatory site on the enzyme; binding of a non-competitive inhibitor here changes enzyme conformation.

• Temperature and pH: Both affect enzyme activity; extremes can cause protein denaturation (loss of structure and function).

• Fever: Can enhance immune response but temperatures above 40°C may cause harmful protein denaturation.

Metabolic Terms and Reactions

• Anabolism: Building up molecules; requires energy.

• Catabolism: Breaking down molecules; releases energy.

• Dehydration Synthesis: Formation of larger molecules by removing water.

• Hydrolysis: Breakdown of molecules by adding water.

• Redox Reactions: Involve electron transfer; OIL RIG (Oxidation Is Loss, Reduction Is Gain).

• Exothermic/Exergonic: Release heat/energy.

• Endothermic/Endergonic: Absorb heat/energy.

ATP and Phosphorylation

• ATP Cycle: ATP is synthesized by phosphorylation and hydrolyzed to ADP by dephosphorylation.

• Phosphorylation Types: Substrate-level, oxidative, and photophosphorylation.

• ATP Synthase: Enzyme in mitochondria (and bacterial membranes) that synthesizes ATP during chemiosmosis.

Cellular Respiration and Fermentation

• Glycolysis: Glucose → 2 pyruvate, 2 ATP, 2 NADH.

• Transition/Bridge Reaction: Pyruvate → Acetyl-CoA, CO2, NADH.

• Krebs Cycle: Acetyl-CoA → CO2, NADH, FADH2, ATP.

• Electron Transport Chain (ETC): NADH and FADH2 donate electrons; O2 is the final electron acceptor, forming H2O. Chemiosmosis drives ATP synthesis.

• ATP Yield: Bacteria: 2-38 ATP (variable); Eukaryotes: ~36 ATP per glucose.

• Anaerobic Respiration: Occurs without O2; less efficient.

• Fermentation: Recycles electron carriers; produces less ATP.

Photosynthesis and Metabolic Diversity

• Photosynthesis: Initiated by electron donation from water or other molecules.

• Cyclic vs. Non-Cyclic Photophosphorylation: Cyclic produces only ATP; non-cyclic produces ATP and NADPH.

• NADPH: Used in photosynthesis; NADH: Used in cellular respiration.

• Metabolic Types:

  • Chemoautotrophs: Energy from chemicals, carbon from CO2.

  • Chemoheterotrophs: Energy and carbon from organic compounds.

  • Photoautotrophs: Energy from light, carbon from CO2.

  • Photoheterotrophs: Energy from light, carbon from organic compounds.

Microbial Growth

Asexual Reproduction and Generation Time

Microbial growth is characterized by reproduction and population increase, measured by generation time.

• Asexual Reproduction: Eukaryotes: mitosis, budding; Prokaryotes: binary fission.

• Generation Time/Doubling Time: Time required for a population to double.

Bacterial Growth Curve

• Four Stages: Lag, Log (Exponential), Stationary, Death.

• Sporulation: Density-dependent; occurs in stationary phase (e.g., Bacillus).

Growth Curve Table

Environmental Factors

• Temperature Optima:

  • Psychrophiles: Low temperatures

  • Mesophiles: Moderate temperatures

  • Thermophiles: High temperatures

  • Hyperthermophiles: Very high temperatures

• Food Storage: Temperature affects microbial growth; refrigeration slows growth.

• pH Range: Bacteria grow only within specific pH and temperature ranges.

Osmotic Environments and Halophiles

• Isotonic: Equal solute concentration inside and outside cell.

• Hypertonic: Higher solute outside; cell loses water.

• Hypotonic: Lower solute outside; cell gains water.

• Nonhalophile: Cannot tolerate high salt.

• Moderate Halophile: Tolerates moderate salt.

• Extreme Halophile: Requires high salt.

Nutrient Sources

• Carbon: Found in cell wall, proteins, nucleic acids.

• Nitrogen: Found in amino acids, nucleic acids.

• Sulfur: Found in some amino acids (e.g., cysteine).

Oxygen Toxicity and Microbial Types

• Protective Reactions: Superoxide dismutase, catalase, peroxidase detoxify reactive oxygen species.

• Microbial Oxygen Requirements:

  • Obligate Aerobes: Require O2

  • Facultative Anaerobes: Can use O2 or not

  • Obligate Anaerobes: Cannot tolerate O2

  • Aerotolerant Anaerobes: Tolerate O2, do not use it

  • Microaerophiles: Require low O2

Culture Media and Microbial Counting

• Defined Media: Exact chemical composition known.

• Complex Media: Contains unknown components.

• Selective Agar: Sabouraud’s dextrose agar selects for fungi.

• Differential Agar: Blood agar differentiates based on hemolysis.

• Selective/Differential Agars:

  • Eosin methylene blue: Selects for Gram-negative, differentiates lactose fermenters.

  • Mannitol agar: Selects for staphylococci, differentiates mannitol fermenters.

  • MacConkey’s agar: Selects for Gram-negative, differentiates lactose fermenters.

• Streak Plate: Used to isolate pure colonies.

• Plate Counts and Serial Dilution: Estimate microbial abundance.

• Filtration: Direct measurement of concentration.

• Most Probable Number (MPN): Statistical estimation of cell numbers.

• Direct Counting: Counting cells under a microscope.

• Spectrophotometry: Indirect measurement based on turbidity.

Microbial Control Terms

• Sterilization: Complete destruction of all microbes.

• Commercial Sterilization: Kills pathogens in food.

• Disinfection: Destroys harmful microbes.

• Antisepsis: Destroys microbes on living tissue.

• Degerming: Removal of microbes from surface.

• Sanitization: Reduces microbial numbers to safe levels.

Genetics

Biofilms

• Biofilm: Community of microbes attached to a surface, embedded in extracellular matrix.

• Locations: Medical devices, natural environments.

• Benefits: Protection from environmental stress, antibiotics.

Genetic Terms

• Genetics: Study of heredity.

• Genes: DNA segments coding for traits.

• Genome: Complete genetic material.

• Genotype: Genetic makeup.

• Phenotype: Observable traits.

DNA Replication, Transcription, and Translation

• DNA Structure: Double helix; nucleotides: adenine, thymine, cytosine, guanine.

• Directionality: 5’ to 3’ ends; DNA synthesis proceeds 5’ → 3’.

• Bonds: Phosphodiester bonds within strand; hydrogen bonds between strands.

• Nucleotide Groups: Phosphate, sugar, base.

• Replication Enzymes:

  • DNA Polymerase III: Synthesizes new DNA.

  • RNA Primase: Lays RNA primer.

  • Helicase: Unwinds DNA.

  • DNA Ligase: Joins Okazaki fragments.

• Leading vs. Lagging Strand: Leading synthesized continuously; lagging in fragments (Okazaki fragments).

• Replication Fork: Site of DNA unwinding and synthesis.

• Origin of Replication: Starting point; bacteria: circular chromosomes, eukaryotes: linear chromosomes.

• Semi-Conservative Replication: Each new DNA has one old and one new strand.

Transcription and RNA Processing

• mRNA Synthesis: RNA polymerase uses template strand; promoter initiates, terminator ends transcription.

• RNA Processing: Eukaryotes: splicing, capping, poly-A tail; Prokaryotes: minimal processing.

• RNA Types: tRNA (transfers amino acids), mRNA (messenger), rRNA (ribosomal).

• tRNA Anticodon: Matches mRNA codon for translation.

• mRNA Codex: Used to determine amino acid sequence.

• Translation Steps: Initiation, elongation, termination.

Genetic Regulation

Gene Regulation and Operons

• Constitutive Genes: Always expressed.

• Regulated Genes: Expression controlled by environment.

• Operon Model (Jacob and Monod): Regulatory gene → promoter → operator → structural genes.

• Operon Components: Promoter, operator, structural genes.

• Inducible vs. Repressible Operons: Inducible: turned on by substrate; repressible: turned off by product.

• Glucose Effect: Presence of glucose represses lac operon.

Quorum Sensing and Alarmones

• Quorum Sensing: Cell communication for biofilm formation, sporulation, virulence.

• Alarmones: Signaling molecules for stress response.

Mutations and Mutagens

• Mutation Types: Silent (no effect), missense (amino acid change), nonsense (stop codon), frameshift (insertion/deletion).

• Chemical Mutagens: Nucleoside analogs, nucleotide-modifying agents, intercalating agents.

• Physical Mutagens: Ionizing radiation (X-rays), non-ionizing radiation (UV).

• UV Damage Resistance: Photoreactivation, nucleotide excision repair.

Example: The lac operon is an inducible operon; it is expressed only when lactose is present and glucose is absent.

Additional info: Some details, such as specific temperature optima for microbial growth, were inferred based on standard microbiology knowledge.