Microbiology Final Exam Review, December 2023 PDF

Microbiology Final Exam Review Tuesday, December 10 8AM TR Ch 3, Cell Structure and Function Overview Synopsis of the bacterial cell The cell membrane The cell envelope and cytoskeleton How bacterial cells divide The nucleoid: structure and expression Specializ...

Microbiology Final Exam Review Tuesday, December 10 8AM TR Ch 3, Cell Structure and Function Overview Synopsis of the bacterial cell The cell membrane The cell envelope and cytoskeleton How bacterial cells divide The nucleoid: structure and expression Specialized structures (vesicles, nanotubes, pili, stalks, flagella) Bacterial flagella and chemotaxis Introduction - Features Distinctive to Each Domain Bacteria and Archaea (Prokaryotes): ○ Lack a nucleus. ○ Bacteria: Have a phospholipid bilayer membrane. ○ Archaea: Unique membrane lipids enabling survival in extreme environments; also live in moderate environments (soil, water, human skin). Eukaryotic Cells: ○ Possess a nucleus. ○ Extensive membranous organelles (endoplasmic reticulum, Golgi complex, mitochondria, chloroplasts). The Bacterial Cell: An Overview Common Traits: ○ Thick, Complex Outer Envelope: Protects from environmental stress and mediates exchange with the environment. ○ Compact Genome: Minimal noncoding DNA, maximizing cell production from limited resources. ○ Tightly Coordinated Cell Functions: Enable high reproduction rates. Biochemical Composition of Bacteria Common Chemical Components: ○ Water (70% of total weight), essential ions (potassium, magnesium, chloride), small organic molecules (lipids, sugars), macromolecules (nucleic acids, proteins). Variable Composition: Depends on species, growth phase, and environmental conditions. Classification of Bacteria Based on Cell Wall Configuration: ○ Gram-Positive Bacteria: Thick cell wall outside the cell membrane (e.g., Bacillus thuringiensis, Streptococcus pyogenes). 1  Microbiology Final Exam Review Tuesday, December 10 8AM TR ○ Gram-Negative Bacteria: Thin cell wall within the periplasm, surrounded by an outer membrane containing phospholipids and lipopolysaccharides (e.g., Escherichia coli). ○ Mycobacteria: Complex, multilayered cell wall (e.g., Mycobacterium tuberculosis). The Cell Membrane (Inner Membrane) Structure and Function: ○ Selectively permeable barrier separating internal components from the external environment. ○ Phospholipid bilayer with lipid-soluble proteins, providing fluidity and consistent thickness (~8 nm). ○ Membrane Lipids: Glycerol with ester links to fatty acids and a phosphoryl head group. ○ Diversity: Varies with environmental conditions; includes variations in phosphoryl head groups and fatty acid side chains. Membrane Lipid Diversity Cardiolipin: A double phospholipid linked by a third glycerol, localizes to cell poles, increases under stress (e.g., starvation, stationary phase). Fatty Acids: ○ Saturated, unsaturated, or polyunsaturated. ○ Cis form of Oleic Acid: Increases membrane fluidity, essential at low temperatures. ○ Cyclopropane Fatty Acid: Forms stiff planar rings, decreasing fluidity, especially during starvation and acid stress. Reinforcing Agents: ○ In eukaryotes: Sterols (e.g., cholesterol). ○ In bacteria: Hopanoids (pentacyclic), adding strength to membranes. Archaea Membrane Lipids Unique Features: ○ Ether links (C-O-C) between glycerol and fatty acids, more stable than ester links, allowing growth at higher temperatures. ○ Tails of the two layers are fused, forming tetraethers, creating a monolayer membrane. Membrane Proteins Functions: ○ Structural support (anchoring cell envelope layers, forming flagella base). ○ Detection of environmental signals (e.g., ToxR in V. cholerae detects acidity and temperature changes). 2  Microbiology Final Exam Review Tuesday, December 10 8AM TR ○ Secretion of virulence factors and communication signals (e.g., NodI and NodJ in nitrogen-fixing rhizobia). ○ Ion transport and energy storage (managing ion gradients). Molecules Crossing the Cell Membrane Mechanisms: ○ Semipermeable Barrier: Allows selective transport essential for survival. ○ Small uncharged molecules (CO2, O2, H2O) permeate easily. ○ Passive Transport: Moves molecules from high to low concentration using concentration gradient. ○ Active Transport: Moves molecules from low to high concentration using energy. The Envelope and Cytoskeleton Protection: ○ The cell envelope includes structural support, typically the cell wall. ○ Additional layers like the outer membrane or S-layer in some bacteria. ○ Exception: Mycoplasmas have a cell membrane without outer layers. The Cell Wall (Sacculus) Structure and Function: ○ Confers shape and rigidity, helps withstand turgor pressure. ○ Composed of peptidoglycan (murein), consisting of long polymers of repeating disaccharides (N-acetylglucosamine and N-acetylmuramic acid) cross-linked with peptides (4-6 amino acids). ○ Peptidoglycan Unique to Bacteria: Target for antibiotics like penicillin (inhibits transpeptidase) and vancomycin (prevents cross-bridge formation). Cell Envelope Composition Gram-Positive Bacteria: ○ Thick cell wall (3-20 layers of peptidoglycan) reinforced by teichoic acids. ○ S-layer: Crystalline layer providing protection and aiding in biofilm formation. ○ Capsule: Slippery layer protecting against phagocytosis. Gram-Negative Bacteria: ○ Thin peptidoglycan layer (1-2 sheets), covered by an outer membrane. ○ Outer Membrane Composition: Inward-facing leaflet: Phospholipid composition, including lipoproteins (e.g., murein lipoprotein). Outward-facing leaflet: Contains lipopolysaccharide (LPS) with components like lipid A, core polysaccharide, and O antigen. Outer Membrane Proteins: Include porins allowing nutrient passage (e.g., OmpF). 3  Microbiology Final Exam Review Tuesday, December 10 8AM TR ○ Periplasm: Aqueous compartment containing the cell wall and specific enzymes/nutrient transporters. ○ S-layer and Capsule: Found in some Gram-negative bacteria (e.g., Campylobacter, Haemophilus influenzae). Bacterial Cytoskeleton Shape-Determining Proteins: ○ FtsZ: Forms the Z-ring for maintaining cell diameter. ○ MreB: Guides peptidoglycan elongation in rod-shaped cells. ○ CreS (Crescentin): Forms a polymer along the inner side of crescent-shaped bacteria. Bacterial Cell Division Process: ○ Highly coordinated growth and formation of all cell parts. ○ Continuous synthesis of RNA and proteins during DNA replication. ○ DNA replication is coordinated with cell wall expansion and daughter cell separation. Cell Division by Septation Septation: ○ Formation of the septum, dividing the cell envelope. ○ FtsZ subunits assemble in a treadmilling pattern, directing septal growth. ○ Requires rapid biosynthesis of envelope components, managed by the divisome (e.g., FtsZ forming the Z-ring, FtsN regulating septum constriction). DNA Organization and Replication Nucleoid: ○ Prokaryotic cells have a nucleoid region extending through the cytoplasm. ○ DNA is attached to the envelope at the origin of replication, with loops of DNA supercoiled and bound to proteins. Transcription and Translation: ○ Ribosomes bind to mRNA and begin translation before transcription completion. ○ Proteins are folded by chaperones, with some secreted or inserted into the membrane. Replication: ○ Begins at the origin (ori) site, with replication forks proceeding outward. ○ Replisome: Complex of DNA polymerase and accessory proteins, replicating DNA at each fork. ○ Spatial orientation of septation determines cocci arrangement (parallel, random, perpendicular planes). Specialized Structures 4  Microbiology Final Exam Review Tuesday, December 10 8AM TR Thylakoids: Folded intracellular membranes in photosynthetic bacteria, packed with chlorophylls and electron carriers for light reactions. Carboxysomes: Polyhedral protein bodies packed with Rubisco for CO2 fixation. Gas Vesicles: Hollow structures collecting gases (H2, CO2), increasing buoyancy for phototrophs. Storage Granules: Include glycogen, PHB, PHA, and sulfur granules for energy storage and avoidance of predation. Pili/Fimbriae: Straight filaments of pilin protein for attachment, motility (twitching), and conjugation. Stalks: Attachment organelle extending from the envelope and cytoplasm, secreting adhesion factors to form holdfasts, enabling iron-oxidizing bacteria to form biofilms in streams. Rotary Flagella Motility: ○ Prokaryotes swim using rotary flagella. ○ Arrangement of Flagella: Peritrichous Cells: Flagella randomly distributed around the cell, rotating together in a bundle behind the swimming cell. Lophotrichous Cells: Flagella at one or both ends of the cell. Monotrichous Cells: A single flagellum at one end. ○ Flagellum Structure: Composed of a spiral filament of protein monomers called flagellin. Rotates by means of a motor driven by the proton motive force. Can rotate either clockwise (CW) or counterclockwise (CCW) relative to the cell. Embedded in the layers of the cell envelope. Chemotaxis Definition: ○ Chemotaxis is the movement of a bacterium in response to chemical gradients. ○ Requires receptors (chemoreceptors) acting like a "nose". Mechanism: ○ Attractants: Cause CCW rotation, flagella bundle together, pushing the cell forward in a "run". ○ Repellents (or absence of attractants): Cause CW rotation, flagellar bundle falls apart, causing a "tumble" where the bacterium briefly stops and changes direction. Behavior: ○ Alternating runs and tumbles cause a "random walk". ○ Receptors detect attractant concentrations (e.g., sugars, amino acids). ○ Increasing attractant concentration prolongs the run, causing net movement toward attractants or away from repellents. Chapter Summary 5  Microbiology Final Exam Review Tuesday, December 10 8AM TR Prokaryotic Traits: ○ Diverse but share fundamental traits and biochemistry. ○ Cell membrane consists of a phospholipid bilayer containing proteins. ○ Bacterial phospholipids are ester-linked; archaeal phospholipids have ether linkages. ○ Gram-negative cell envelope is more complex than that of Gram-positive cells. DNA Organization: ○ DNA is organized into loops in the nucleoid. ○ Transcription and translation are coupled. Cell Division: ○ Most bacteria divide by fission. ○ Cell growth and DNA replication are coordinated. Specialized Structures: ○ Bacteria may have vesicles, nanotubes, thylakoids, carboxysomes, and storage granules. ○ Pili and stalks are used for attachment. ○ Flagella are rotary appendages used for movement and chemotaxis. 6