Metabolism

Gibbs Free Energy and Enzyme Catalysis

Metabolic reactions are governed by changes in Gibbs free energy, which determines whether a reaction is spontaneous. Enzymes catalyze reactions by lowering the activation energy, increasing reaction speed without altering the overall energy change between reactants and products.

• Gibbs Free Energy Graph: Shows the energy of reactants and products; the difference indicates spontaneity.

• Activation Energy: The energy required to initiate a reaction; enzymes lower this barrier.

• Enzyme Function: Enzymes do not change the net energy difference between reactants and products.

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

• Cofactors vs. Coenzymes: Cofactors are inorganic (e.g., metal ions), coenzymes are organic (e.g., NAD+).

• Apoenzyme: Protein portion of an enzyme without its cofactor.

• Holoenzyme: Complete, active enzyme with its cofactor.

• Competitive Inhibitor: Binds to the active site, blocking substrate.

• Non-Competitive Inhibitor: Binds to an allosteric site, changing enzyme shape and reducing activity.

• Allosteric Site: A site other than the active site where molecules can bind and affect enzyme function.

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

• Fever: Can inhibit bacterial growth, but temperatures above 40°C may cause harmful denaturation of human proteins.

Key Terms: Anabolism (building molecules), Catabolism (breaking down molecules), Dehydration Synthesis (removing water to build), Hydrolysis (adding water to break).

Redox Reactions and Energy Terms

Redox reactions involve electron transfer; one molecule is oxidized (loses electrons), another is reduced (gains electrons). Remember: OIL RIG (Oxidation Is Loss, Reduction Is Gain).

• Exothermic: Releases heat.

• Exergonic: Releases energy.

• Endothermic: Absorbs heat.

• Endergonic: Absorbs energy.

ATP and Phosphorylation

ATP is the main energy currency. It is generated by phosphorylation reactions:

• Substrate-level phosphorylation

• Oxidative phosphorylation

• Photophosphorylation

ATP cycle involves phosphorylation (adding phosphate) and dephosphorylation (removing phosphate).

Summary of Glycolysis, Bridge Reaction, Krebs Cycle

These pathways break down glucose and generate ATP and electron carriers.

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

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

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

• CO2 Release: Occurs during bridge and Krebs cycle steps.

Electron Transport Chain and Chemiosmosis

Electron carriers (NADH, FADH2) donate electrons to the chain; O2 is the final electron acceptor, forming H2O. Chemiosmosis uses the proton gradient to drive ATP synthesis via ATP synthase.

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

• ATP Synthase: Enzyme in mitochondrial membrane (or bacterial membrane) that synthesizes ATP.

Anaerobic Respiration and Fermentation

Anaerobic respiration occurs without O2, yielding less ATP. Fermentation recycles electron carriers and produces various end products.

• Fermentation: Allows recycling of NADH to NAD+.

• Multiple Pathways: Some bacteria use mixed acid fermentation.

Catabolic Efficiency Comparison Table

Photosynthesis

Photosynthesis uses light energy to drive electron transfer and ATP synthesis. NADPH is used in photosynthesis, NADH in cellular respiration.

• Electron Donor: Water (H2O) in oxygenic photosynthesis.

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

• Bacterial Photosynthesis: Can occur in aerobic or anaerobic environments.

Metabolic Classification Table

Microbial Growth

Asexual Reproduction

Microbes reproduce asexually. Eukaryotes use mitosis, budding, and fragmentation; prokaryotes use binary fission.

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

Bacterial Growth Curve

Bacterial populations follow a four-stage growth curve: lag, log, stationary, and death.

• Lag Phase: Adaptation, no growth.

• Log Phase: Exponential growth.

• Stationary Phase: Growth rate equals death rate; sporulation may occur.

• Death Phase: Decline in population.

Temperature and pH Effects

Microbes have optimal temperature and pH ranges; outside these, growth is inhibited.

• Psychrophiles: Optimal at low temperatures.

• Mesophiles: Optimal at moderate temperatures.

• Thermophiles: Optimal at high temperatures.

• Hyperthermophiles: Optimal at very high temperatures.

• Clinical Implications: Proper food storage prevents growth of pathogens.

Osmotic Environments

Solute concentration affects cell water balance.

• Isotonic: Equal solute inside and outside.

• 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.

Microbial Nutrient Sources

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

• Nitrogen: Found in amino acids, nucleic acids.

• Sulfur: Found in some amino acids and vitamins.

Oxygen Toxicity and Protective Enzymes

Some microbes produce enzymes to detoxify reactive oxygen species.

• Superoxide Dismutase

• Catalase

• Peroxidase

Oxygen Requirements

Microbes vary in their need for oxygen.

• 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 Types

• 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 Agar: Eosin methylene blue, Mannitol agar, MacConkey’s agar select and differentiate based on microbial properties.

Microbial Abundance Estimation

• Streak Plate: Isolates colonies.

• Plate Counts & Serial Dilution: Estimate abundance.

• Filtration: Direct measurement of concentration.

• Most Probable Number (MPN): Statistical estimation.

• Direct Counting: Microscopic count.

• Spectrophotometry: Indirect measurement via turbidity.

Microbial Control Terms

• Sterilization: Complete removal of all microbes.

• Commercial Sterilization: Kills Clostridium botulinum spores.

• Disinfection: Removal of pathogens.

• Antisepsis: Removal of pathogens from living tissue.

• Degerming: Removal of microbes from a limited area.

• Sanitization: Lowering microbial counts to safe levels.

Genetics

Biofilms

Biofilms are communities of microbes attached to surfaces, providing protection and enhanced survival.

• Locations: Medical devices, natural environments.

• Benefits: Protection from antibiotics, environmental stress.

Genetic Terms

• Genetics: Study of heredity.

• Genes: DNA segments coding for traits.

• Genome: Entire genetic content.

• Genotype: Genetic makeup.

• Phenotype: Observable traits.

DNA Replication, Transcription, Translation

Genetic information flows from DNA to RNA to protein.

• DNA Structure: Double helix; nucleotides (A, T, C, G); 5’ to 3’ directionality.

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

• Nucleotide Groups: Phosphate, sugar, base.

• Enzymes: DNA Polymerase III (synthesis), RNA Primase (primer), Helicase (unwinding), DNA Ligase (joining fragments).

• Replication: Semi-conservative; leading and lagging strands; Okazaki fragments; replication fork; origin of replication.

• Chromosome Structure: Bacteria: circular; Eukaryotes: linear.

DNA Replication Models Table

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: mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

• tRNA: Has anticodon matching mRNA codon.

• Translation Steps: Initiation, elongation, termination.

Genetic Regulation

• Constitutive Genes: Always expressed.

• Regulated Genes: Expressed as needed.

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

• Operon Components: Promoter, operator, structural genes.

• Inducible Operon: Activated by substrate presence (e.g., lac operon).

• Repressible Operon: Turned off by product presence (e.g., trp operon).

• Catabolite Repression: Presence of glucose inhibits lac operon.

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

• Alarmones: Signaling molecules for stress response.

Mutations and Mutagens

• Silent Mutation: No effect on protein.

• Missense Mutation: Changes one amino acid.

• Nonsense Mutation: Creates stop codon.

• Frameshift Mutation: Alters reading frame.

• Chemical Mutagens: Nucleoside analogs (substitution), nucleotide-modifying agents (alter bases), intercalating agents (insertions).

• Physical Mutagens: Ionizing radiation (breaks DNA), non-ionizing radiation (UV, causes thymine dimers).

• UV Damage Resistance: Photoreactivation and nucleotide excision repair.

Example: The lac operon is an inducible operon regulated by the presence of lactose and glucose.

Additional info: Academic context and definitions were expanded for clarity and completeness.