Metabolism Basics

Definition and Role in Cells

Metabolism refers to all chemical reactions that occur within a living organism to maintain life. It is divided into two main processes:

• Anabolism: The synthesis of complex molecules from simpler ones, requiring energy input.

• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy.

These processes are essential for cell growth, reproduction, and maintenance.

Redox Reactions

• Oxidation: Loss of electrons from a molecule.

• Reduction: Gain of electrons by a molecule.

• The reducing agent donates electrons, while the oxidizing agent accepts electrons.

Example: In cellular respiration, glucose is oxidized and oxygen is reduced.

Oxidized and Reduced Forms

• NAD+ is the oxidized form; NADH is the reduced form.

• FAD is the oxidized form; FADH2 is the reduced form.

ATP and Phosphorylation

• ATP (Adenosine Triphosphate): The primary energy carrier in cells.

• Substrate-level phosphorylation: Direct transfer of a phosphate group to ADP from a substrate.

• Oxidative phosphorylation: ATP synthesis using energy derived from the electron transport chain.

Function of NAD+ and FAD: Electron carriers in metabolic pathways.

Enzymes

Categories and Functions

• Enzymes are biological catalysts that speed up chemical reactions in cells.

• Six basic categories: oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases.

Enzyme-Substrate Interactions

• Active site: The region on the enzyme where the substrate binds.

• Enzyme specificity: Each enzyme acts on a specific substrate.

• Enzyme inhibition: Can be competitive, non-competitive, or feedback inhibition.

Factors affecting enzyme activity: Temperature, pH, inhibitors.

Catabolism

Aerobic vs. Anaerobic Respiration and Fermentation

• Aerobic respiration: Uses oxygen as the final electron acceptor; produces the most ATP.

• Anaerobic respiration: Uses other molecules (e.g., nitrate, sulfate) as final electron acceptors.

• Fermentation: Partial oxidation of glucose without an electron transport chain; produces less ATP.

Steps of Cellular Respiration

1. Glycolysis: Glucose is broken down into pyruvate, producing ATP and NADH.

2. Krebs Cycle (Citric Acid Cycle): Pyruvate is further oxidized, generating ATP, NADH, and FADH2.

3. Electron Transport Chain: Electrons from NADH and FADH2 are transferred through protein complexes, creating a proton gradient that drives ATP synthesis.

Fermentation: Regenerates NAD+ for glycolysis in the absence of oxygen; end products include lactic acid or ethanol.

Growth Requirements

Chemical and Energy Requirements

• Energy sources: Light (phototrophs) or chemicals (chemotrophs).

• Carbon sources: CO2 (autotrophs) or organic compounds (heterotrophs).

• Oxygen requirements: Obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles, aerotolerant anaerobes.

• Other requirements: Nitrogen, phosphorus, sulfur, trace elements, growth factors.

Temperature and pH

• Microbes have minimum, optimum, and maximum growth temperatures.

• Categories: psychrophiles (cold-loving), mesophiles (moderate), thermophiles (heat-loving), hyperthermophiles (extreme heat).

• pH categories: neutrophiles (neutral), acidophiles (acidic), alkaliphiles (basic).

Relationships Between Cells

Symbiotic and Non-Symbiotic Relationships

• Symbiosis: Close association between two organisms.

• Types: mutualism (both benefit), commensalism (one benefits, other unaffected), parasitism (one benefits, one harmed).

• Non-symbiotic: Organisms are free-living; relationships are not required for survival.

Antagonistic and Synergistic Relationships

• Antagonism: One organism inhibits or destroys another.

• Synergism: Cooperative interaction for mutual benefit.

Biofilms and Quorum Sensing

• Biofilm: Community of microorganisms attached to a surface, embedded in a self-produced matrix.

• Quorum sensing: Cell-to-cell communication to coordinate activity based on population density.

Culturing Microorganisms

Isolation Techniques and Media

• Techniques: streak plate, pour plate, spread plate.

• Media types: selective, differential, enriched, complex, defined.

• Choice of media depends on the organism and experimental goal.

Growth of Microbial Populations

Binary Fission and Growth Curve

• Binary fission: Asexual reproduction in prokaryotes; one cell divides into two identical cells.

• Growth curve phases: Lag, log (exponential), stationary, death.

Measuring Microbial Growth

• Methods: direct cell count, viable plate count, turbidity measurement.

• Cell number increases exponentially during log phase.

Replication of Genomes

DNA Structure and Replication

• Genome: The complete set of genetic material in an organism.

• Prokaryotic vs. Eukaryotic genomes: Prokaryotes have circular DNA; eukaryotes have linear chromosomes.

• DNA replication: Semi-conservative process; each new DNA molecule has one old and one new strand.

• Key enzymes: DNA polymerase, helicase, primase, ligase.

• Replication proceeds in the 5' to 3' direction.

Transcription and Translation

• Transcription: Synthesis of RNA from a DNA template.

• Translation: Synthesis of proteins from mRNA at the ribosome.

• Codon: Three-nucleotide sequence on mRNA that codes for an amino acid.

• Anticodon: Complementary sequence on tRNA.

Regulation of Genetic Expression

Gene Regulation Mechanisms

• Constitutive genes: Expressed continuously.

• Inducible genes: Expressed only in the presence of an inducer (e.g., lac operon).

• Repressible genes: Expression is inhibited by a specific molecule (e.g., trp operon).

Mutation of Genes

Types and Effects of Mutations

• Silent mutation: No change in amino acid sequence.

• Nonsense mutation: Introduces a stop codon, truncating the protein.

• Missense mutation: Changes one amino acid in the protein.

• Mutagens: Agents that cause mutations (e.g., chemicals, radiation).

Genetic Recombination

Mechanisms and Plasmids

• Recombinant organism: Contains DNA from two different sources.

• Mechanisms: Transformation (uptake of naked DNA), transduction (bacteriophage-mediated), conjugation (direct transfer via pilus).

• Plasmid: Small, circular DNA molecule independent of the chromosome; often carries antibiotic resistance genes.

Summary Table: Types of Microbial Metabolism

Key Equations

• ATP hydrolysis:

• General redox reaction:

• Binary fission (exponential growth):