Microbiology Review_Study Sheets.pdf

Chapter 1 Evolution of Microbes 1. Life on Earth Earth is about 4.5 billion years old. Microbes appeared approximately 3.5 billion years ago. 2. Microbial Diversity Metabolic diversity: Microbes can respire aerobically, photosynthesize, or use inorganic matter for energy...

Chapter 1 Evolution of Microbes 1. Life on Earth Earth is about 4.5 billion years old. Microbes appeared approximately 3.5 billion years ago. 2. Microbial Diversity Metabolic diversity: Microbes can respire aerobically, photosynthesize, or use inorganic matter for energy. Environmental diversity: Microbes thrive in extreme conditions like geothermal vents or the Arctic. Examples include: ○ Deferribacter desulfuricans (geothermal vents) ○ Polaribacter (Arctic environments) ○ Thiobacillus ferrooxidans (varied pH environments) 3. Characteristics of Microorganisms Microorganisms are typically too small to be seen by the naked eye, though there are exceptions like Thiomargarita magnifica and some filamentous fungi. They are generally simple in construction, lacking highly differentiated cells and tissues. 4. Types of Microbes Prokaryotes: Lack a true membrane-delimited nucleus, e.g., bacteria. Eukaryotes: Have membrane-enclosed nuclei, are more complex, and usually larger, e.g., fungi. 5. Classification Systems Microbial classification has been greatly influenced by developments in electron microscopy, biochemistry, and molecular biology. 3 Domain System: ○ Bacteria: Single-celled, with a cell wall containing peptidoglycan, no membrane-bound nucleus. ○ Archaea: Unique rRNA sequences, lacking peptidoglycan, with unique membrane lipids. ○ Eukarya: Includes animals, plants, fungi, and protists. 6. Acellular Infectious Agents Viruses: Smallest microbes, require a host to replicate. Viroids: Infectious RNA. Prions: Infectious proteins. 7. Origin of Life and RNA World Hypothesis Early life may have been RNA-based due to its ability to store and replicate genetic information and catalyze chemical reactions. LUCA (Last Universal Common Ancestor) is thought to have diverged into Bacteria, Archaea, and Eukarya. 8. Evolution of Eukaryotes Endosymbiotic hypothesis: Certain organelles (e.g., mitochondria) in eukaryotes originated from bacteria that lived inside another cell. 9. Microscopy and Early Discoveries Antony van Leeuwenhoek: The first person to observe microorganisms. Louis Pasteur: Disproved spontaneous generation with the famous swan-neck flask experiment. 10. Germ Theory and Disease Heinrich de Bary: Showed fungi caused diseases in crops. Louis Pasteur: Demonstrated that microorganisms are responsible for fermentation and developed the process of pasteurization. Robert Koch: Established the link between microbes and disease using Koch’s postulates. 11. Koch’s Postulates (Key criteria to link a microbe to a disease): 1. The microorganism must be present in all cases of the disease. 2. It must be isolated and grown in pure culture. 3. It should cause the same disease when introduced to a healthy host. 4. The same organism must be isolated from the newly diseased host. 12. Microbial Techniques and Innovations Development of tools like culture media, Petri dishes, and methods to isolate microorganisms.  Attenuation: Pathogens lose their ability to cause disease over time, a discovery that led to vaccine development (e.g., rabies, anthrax). 13. Fields in Microbiology Medical: Study of diseases. Epidemiology: Public health and disease distribution. Immunology: Defense against pathogens. Agricultural/Food: Role of microbes in crops and food production. Industrial: Use of microbes in industry (e.g., antibiotics, biofuels). 14. Microbial Taxonomy and Classification Taxonomy: Organisms are classified into groups based on similarities. ○ Binomial nomenclature (Genus and species), e.g., Escherichia coli. ○ Strains in bacteria: Descendants of a pure microbial culture. Biovars: Differ in biology/physiology. Morphovars: Differ in morphology. Serovars: Differ in antigenic properties. 15. Modern Classification Methods Polyphasic taxonomy: Uses multiple characteristics for classification. Molecular techniques: Advances in DNA/RNA sequencing allow classification based on genetic material (e.g., SSU rRNA sequencing). 16. Bergey's Manual A standard reference for bacterial identification, first published in 1923, now available online. Chapter 2 Microscopy 1. Introduction to Microscopy Microscopes enable observation of objects too small to be seen with the naked eye. Different types of microscopes use light, electrons, or scanning probes to achieve magnification. 2. Light and Refraction Light refraction occurs when light passes from one medium to another, bending due to differences in refractive indices. Refractive index is a measure of how much a substance slows down light. 3. Lenses and Magnification Lenses focus light at a point called the focal point (F). Focal length (f) is the distance between the lens center and the focal point; shorter focal lengths result in higher magnification. Microscopes use objective and ocular lenses to magnify the specimen. Total magnification is determined by multiplying the magnifications of these two lenses. 4. Resolution Resolution is the ability of a lens to distinguish two closely spaced objects. Immersion oil is often used to enhance resolution by reducing light refraction, matching the refractive index of the glass slide. 5. Types of Light Microscopes 1. Bright-field microscope: ○ Produces a dark image against a bright background. ○ Can be used with stained or unstained specimens. 2. Dark-field microscope: ○ Produces a bright image against a dark background. ○ Suitable for observing living, unstained specimens. ○ Example: Observing Treponema pallidum (causes syphilis). 3. Phase-contrast microscope: ○ Converts phase shifts in light to differences in light intensity, useful for visualizing living cells without staining. 4. Fluorescence microscope: ○ Produces a bright image by detecting fluorescent light emitted by the specimen, typically stained with fluorochromes. ○ Useful for identifying specific structures or organisms using different fluorescent dyes. 6. Fixation and Staining Fixation preserves specimens by holding their structures in place. ○ Heat fixation: Common for microbes; preserves morphology but may distort internal structures. ○ Chemical fixation: Used for larger, delicate organisms (e.g., protists). Staining increases contrast and makes internal/external structures more visible. ○ Dyes have two components: chromophore group (color) and binding properties (ionic, covalent, hydrophobic). 7. Types of Staining 1. Simple Staining: ○ Uses a single dye to determine the size, shape, and arrangement of microorganisms. 2. Differential Staining: ○ Uses multiple dyes to distinguish between different groups or structures. ○ Gram Staining: The most widely used differential stain, classifying bacteria as Gram-positive or Gram-negative based on cell wall structure. Process: Crystal violet → Iodine → Alcohol (decolorizer) → Safranin (counterstain). ○ Acid-fast Stain: Used for bacteria with waxy cell walls containing mycolic acids, e.g., Mycobacterium tuberculosis. ○ Endospore Stain: Identifies spore-forming bacteria by forcing dye into spores using heat. ○ Capsule Stain: Highlights the protective polysaccharide layer (capsule) of some bacteria. ○ Flagella Stain: Visualizes bacterial flagella to determine motility. 8. Electron Microscopy Uses an electron beam instead of light, providing much higher resolution. 1. Transmission Electron Microscope (TEM): ○ Electrons pass through a thin specimen, creating an image based on varying electron densities. ○ Provides detailed internal structure images but requires thin-sectioned, non-living samples. 2. Scanning Electron Microscope (SEM): ○ Electrons interact with the surface of a specimen, producing detailed 3D images of the surface. ○ Requires samples to be coated with a thin layer of metal. 9. Scanning Probe Microscopy 1. Scanning Tunneling Microscope (STM): ○ Can magnify up to 100 million X by scanning a probe across the surface and measuring current fluctuations. ○ Used to visualize individual atoms on a solid surface. 2. Atomic Force Microscope (AFM): ○ Developed to improve upon STM. ○ Works by maintaining a constant distance between a sharp probe and the sample surface. ○ Ideal for non-conductive specimens like biological molecules (e.g., aquaporin protein). Chapter 3 Cell Structure 1. Prokaryotes vs. Eukaryotes The term "prokaryote" is controversial, as it focuses on what is lacking compared to eukaryotes. Traditionally, prokaryotes included Bacteria and Archaea, but some Archaea (e.g., Planctomycetes) have membrane-bound genetic material and organelles like the anammoxosome, involved in energy metabolism. 2. Bacterial Shape and Arrangement Coccus (round): ○ Can form single cells, clusters (Staphylococcus), chains (Streptococcus), tetrads (Micrococcus), or cubes (Sarcina). ○ Example: Neisseria gonorrhea (diplococcus). Bacillus (rod-shaped): ○ Can be single, paired (diplobacilli), or in chains. ○ Example: Bacillus megaterium. Vibrio (comma-shaped): Example: Vibrio cholerae (causes cholera). Spirillum (rigid spiral): Example: Helicobacter pylori (causes ulcers). Spirochete (flexible spiral): Example: Treponema pallidum (causes syphilis). Pleomorphic: Variable shapes, e.g., Corynebacteria. 3. Bacterial Cell Size Smallest: 0.3 μm (Mycoplasma). Average rod: 1.1 - 1.5 x 2 - 6 μm (E. coli). Very large: 600 x 80 μm (Epulopiscium fishelsoni). Very, very large: Up to 1 cm (Thiomargarita magnifica). 4. Bacterial Cell Envelope Consists of: ○ Plasma membrane: Selectively permeable, involved in nutrient/waste regulation, and crucial for metabolic processes. ○ Cell wall: Maintains shape, provides protection, and contributes to pathogenicity. ○ Layers outside the cell wall: Capsule, slime layer, or S-layer. 5. Plasma Membrane Structure Lipid bilayer with floating proteins. Proteins can be peripheral (loosely attached) or integral (embedded in the membrane). Functions: Barrier, nutrient transport, energy generation. 6. Movement of Molecules In and Out of the Cell Passive diffusion: Movement from high to low concentration (H2O, O2, CO2). Facilitated diffusion: Transport proteins assist movement without energy. Active transport: Energy-dependent, moving molecules against the gradient. Includes primary (ATP-driven) and secondary (ion gradient-driven) active transport. 7. Group Translocation and Iron Uptake Group translocation: Molecules are chemically modified as they are transported across the membrane. Iron uptake: Bacteria secrete siderophores to bind ferric ions, aiding iron transport into the cell. 8. Bacterial Cell Wall Peptidoglycan (PG): ○ Rigid structure outside the plasma membrane. ○ Composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). ○ Gram-positive bacteria: Thick PG layer, stain purple. ○ Gram-negative bacteria: Thin PG layer, surrounded by an outer membrane (OM), stain pink. Teichoic acids (Gram-positive): Provide rigidity, help maintain structure, and may bind to host cells. Lipopolysaccharides (LPS) (Gram-negative): Stabilize the outer membrane, contribute to the negative charge, and protect against host defenses. 9. Gram Staining A differential stain based on cell wall differences: ○ Crystal violet: Primary stain, binds to negatively charged cell walls. ○ Iodine: Mordant, enhances dye retention. ○ Alcohol: Decolorizer, removes dye from Gram-negative cells. ○ Safranin: Counterstain, colors Gram-negative cells pink. 10. Layers Outside the Cell Wall Capsule: Well-organized, composed of polysaccharides, resists desiccation and phagocytosis. Slime layer: Less organized, easily removed, associated with motility. S-layer: Regular protein layer, contributes to structural integrity and environmental protection. 11. Bacterial Cytoplasm Includes cytoskeleton, inclusions, ribosomes, nucleoid, and plasmids. 12. Cytoskeleton Bacterial cells have cytoskeletal proteins that serve similar functions to eukaryotic cytoskeletons, providing structure and assisting with cell division and shape maintenance. 13. Inclusions Storage inclusions: Store nutrients, energy, or building blocks for later use (e.g., glycogen, polyphosphate, carbon storage). Gas vacuoles: Provide buoyancy in aquatic environments. Magnetosomes: Help bacteria orient using Earth's magnetic field. 14. Ribosomes 70S ribosomes in bacteria (30S + 50S subunits). Sites of protein synthesis. 15. Nucleoid The region containing the bacterial chromosome, usually a single circular DNA molecule. Plasmids: Small, extrachromosomal DNA that replicate independently, often carrying genes for antibiotic resistance or virulence factors. 16. Bacterial Motility Bacteria move in response to environmental stimuli (e.g., temperature, light, oxygen). Types of movement: ○ Swimming (flagella-based). ○ Swarming. ○ Twitching (pilus-based). ○ Gliding (surface-based). 17. Pili/Fimbriae and Flagella Pili/Fimbriae: Short, hair-like structures used for attachment to surfaces and in some cases for DNA transfer (sex pili). Flagella: Long, thread-like appendages used for locomotion. Can have different arrangements (monotrichous, lophotrichous, etc.). 18. Endospores Endospores: Dormant, tough structures formed by some bacteria (e.g., Bacillus anthracis, Clostridium botulinum) for survival under harsh conditions. Resistant to extreme environments, including heat, radiation, and desiccation. Sporulation: The process of endospore formation. When conditions improve, the spore germinates and returns to a vegetative state.