Microbiology PDF

Structure and Morphology 1. Basic Structure, Composition, and Function of Cell Components Cell Membrane: Phospholipid bilayer with proteins; selective permeability, signal transduction. Cell Wall: ○ Bacteria: Peptidoglycan. ○ Archaea: Pseudomurein or S-laye...

Structure and Morphology 1. Basic Structure, Composition, and Function of Cell Components Cell Membrane: Phospholipid bilayer with proteins; selective permeability, signal transduction. Cell Wall: ○ Bacteria: Peptidoglycan. ○ Archaea: Pseudomurein or S-layer proteins. ○ Eukaryotes: Cellulose (microalgae), chitin (fungi). Flagella: Motility; different structures in bacteria (rotary) and eukaryotes (whip-like). Pilus/Fimbria: Attachment and conjugation. Nucleoid: Bacterial/archaeal DNA region. Cytoplasm: Metabolic activity site. Specialized Structures: ○ Gas Vesicles: Buoyancy. ○ Endospores: Survival in harsh conditions (e.g., Bacillus, Clostridium). ○ Carboxysomes: CO2 fixation. ○ Eyespots: Light detection (eukaryotic algae). 2. Gram (+), Gram (-), and Acid-Fast Bacteria Gram (+): Thick peptidoglycan, teichoic acids; purple stain. Gram (-): Thin peptidoglycan, outer membrane with LPS; pink stain. Acid-Fast: Mycolic acids; Ziehl-Neelsen staining (e.g., Mycobacterium). 3. Viral Structures Capsid: Protein shell; helical or icosahedral. Envelope: Lipid bilayer (not all viruses). Genome: DNA or RNA, single- or double-stranded. 4. Locomotion (State/Nationals Only) Swimming: Flagellar motion. Gliding: Surface contact motility. Chemotaxis: Movement in response to chemical gradients. Phototaxis: Movement toward light. Culture and Growth 1. Culturing Bacteria  Methods: ○ Liquid cultures: Growth rate studies. ○ Solid media: Isolation of colonies. Media: ○ Selective: Inhibit unwanted microbes. ○ Differential: Distinguish microbes based on biochemical properties. 2. Bacterial Growth Curves Lag Phase: Adaptation. Log Phase: Exponential growth. Stationary Phase: Nutrient depletion. Death Phase: Decline. 3. Cell Population Calculations CFU (Colony-Forming Units):. Optical Density: Proportional to cell density. 4. Antibiotics and Resistance (State/Nationals Only) Classes: ○ Penicillins: Target cell wall synthesis. ○ Tetracyclines: Inhibit protein synthesis. Resistance Mechanisms: ○ Efflux pumps, target modification, enzymatic degradation. 5. Sterilization and Disinfection Techniques: ○ Heat (autoclaving): Best for sterilizing heat-resistant instruments and media in laboratory settings. ○ Radiation (UV): Ideal for surface sterilization and air disinfection in healthcare or laboratory environments. ○ Filtration: Used for sterilizing heat-sensitive liquids, such as vaccines or enzymes, by removing microbes without heat. ○ Chemicals (alcohol, bleach): Effective for disinfecting surfaces, equipment, and hands; bleach is particularly useful against bacterial spores. 6. Limitations of Culture-Based Approaches Misses unculturable microbes; bias towards fast-growing species. Molecular Biology 1. Bacterial Cell Division Binary Fission: ○ DNA replication begins at the origin. ○ Key proteins: DnaA (initiator), DNA polymerase (elongation). Rolling Circle Replication (State/Nationals): Plasmids and some viruses. 2. Transcription and Translation Transcription: ○ Enzyme: RNA polymerase. ○ Promoters and terminators. Translation: ○ Ribosomes, tRNA, codons. 3. Gene Regulation (lac and trp Operons) Lac Operon: Inducible; activated by lactose. Trp Operon: Repressible; turned off by tryptophan. 4. Recombinant DNA (State/Nationals) Applications: Producing insulin, GMOs. Metabolism and Applications 1. Metabolic Strategies Energy Sources: ○ Phototrophs: Light. ○ Chemotrophs: Chemical compounds. Carbon Sources: ○ Autotrophs: CO2. ○ Heterotrophs: Organic compounds. 2. Key Processes Fermentation: Pyruvate as an electron acceptor. Photosynthesis: Oxygenic in algae and cyanobacteria. Nitrogen Fixation: Enzyme nitrogenase; rhizosphere microbes. 3. Applications Fermentation: Bread, soy sauce, sauerkraut.  Biofuels: Photosynthetic microbes. Nitrogen Fixation: Agriculture. 4. Alternative Electron Donors/Acceptors (State/Nationals) Winogradsky Column: Model for microbial ecosystems. Evolution and Ecology 1. Endosymbiotic Theory Origin of mitochondria and chloroplasts from ancient symbiotic bacteria. 2. Adaptations to Extremes Temperature: Heat-stable enzymes (e.g., Thermus aquaticus). Salinity: Compatible solutes. pH: Acidophiles and alkaliph Evolution and Ecology (Continued) 3. Lytic and Lysogenic Viral Life Cycles Lytic Cycle: ○ Virus infects host, hijacks cellular machinery to produce new viruses. ○ Results in host cell lysis and release of progeny viruses. ○ Example: Escherichia virus T4. Lysogenic Cycle: ○ Viral genome integrates into host DNA as a prophage, remaining dormant. ○ Environmental triggers may induce lytic cycle. ○ Example: Escherichia virus Lambda. 4. Genomic Analysis for Functional Potential and Evolution Comparative genomics reveals evolutionary relationships. Identification of genes encoding specific metabolic or pathogenic traits. Tools: BLAST, phylogenetic tree construction, and genome annotation. 5. Horizontal Gene Transfer Mechanisms Transduction: DNA transfer via bacteriophages. Conjugation: Plasmid-mediated transfer through pilus. Transformation: Uptake of free DNA from the environment. Role in evolution: Rapid acquisition of new traits, including antibiotic resistance. 6. 16S Amplicon Sequencing Applications: ○ Determine bacterial community composition. ○ Measure alpha diversity (within-sample) and beta diversity (between-sample). PCR Process: Amplify 16S rRNA gene regions using specific primers. Limitations: Cannot detect functional genes or non-bacterial microbes. 7. Microbial Community Interactions Cooperation/Mutualism: Both species benefit (e.g., nitrogen-fixing bacteria and plants). Commensalism: One species benefits without affecting the other. Predation: One species preys on another (e.g., Bdellovibrio). Parasitism: One species benefits at the expense of the other. Interactions mediated by metabolic pathways (e.g., production of siderophores or signaling molecules). 8. Advanced Sequencing Techniques (State/Nationals Only) Metagenomics: DNA-based; identifies community genetic potential. Metatranscriptomics: RNA-based; identifies active metabolic pathways. Meta-proteomics and Metabolomics: Study proteins and metabolites in microbial communities. Appropriate Use: Depends on experimental goals (e.g., metatranscriptomics for activity analysis). 9. Bacterial Defense Mechanisms (State/Nationals Only) Restriction-Modification (RM) Systems: ○ Restriction enzymes cleave foreign DNA at specific sites. ○ Host DNA protected by methylation. CRISPR-Cas Systems: ○ Adaptive immunity; stores viral DNA sequences in CRISPR loci. ○ Cas proteins recognize and cleave matching viral DNA during subsequent infections. Microbes and Agents List 1. Bacteria Escherichia coli: Model organism; some strains pathogenic. Rickettsia rickettsii: Causes Rocky Mountain spotted fever. Mycobacterium leprae: Causes leprosy. Mycobacterium tuberculosis: Causes tuberculosis; acid-fast.  Microcystis aeruginosa: Cyanobacterium; produces toxins in water blooms. Staphylococcus aureus: Skin infections, MRSA. Helicobacter pylori: Associated with gastric ulcers and cancer. 2. Archaea Pyrococcus furiosus: Hyperthermophile; thrives at >100°C. Methanococcus sp.: Produces methane under anaerobic conditions. 3. Eukaryotes Plasmodium falciparum: Causes malaria; transmitted by Anopheles mosquitoes. Saccharomyces cerevisiae: Baker’s yeast; used in brewing and baking. Nannochloropsis sp.: Microalgae; biofuel production. Paramecium sp.: Ciliated protist; freshwater environments. 4. Viruses and Other Subcellular Agents Escherichia virus T4: Model lytic bacteriophage. Escherichia virus Lambda: Model lysogenic bacteriophage. Measles virus: Causes measles; ssRNA genome. Smallpox virus: Causes smallpox; dsDNA genome. SARS-CoV-2 virus: Causes COVID-19; ssRNA genome. Human Immunodeficiency Virus (HIV): Retrovirus; causes AIDS. Major Prion Protein: Misfolded proteins causing diseases like Creutzfeldt-Jakob Disease (CJD).