Microbiology Study Guide: Metabolism, Enzymes, Catabolism, Growth, Genetics, and More

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

Type	Energy Source	Carbon Source	Example Organism
Photoautotroph	Light	CO2	Cyanobacteria
Chemoautotroph	Inorganic chemicals	CO2	Nitrosomonas
Photoheterotroph	Light	Organic compounds	Rhodobacter
Chemoheterotroph	Organic chemicals	Organic compounds	Escherichia coli

Key Equations

• ATP hydrolysis: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

• General redox reaction: $\text{A}_{\text{red}} + \text{B}_{\text{ox}} \rightarrow \text{A}_{\text{ox}} + \text{B}_{\text{red}}$

• Binary fission (exponential growth): $N_t = N_0 \times 2^n$