Prokaryotic Cell Biology

Prokaryotic Cell Shapes

• Prokaryotic cells feature a variety of shapes that include cocci (spherical), bacilli (rod-shaped), spirilla (spiral), vibrios (comma-shaped), spirochetes (flexible spiral), filamentous (long threads), and pleomorphic (variable) types.

Importance and Limitations of Small Cell Size

• Small cell size in prokaryotes is crucial for a high surface area-to-volume ratio, facilitating efficient nutrient uptake and rapid reproduction.
• Cell size is limited by the necessity to house essential components like DNA and ribosomes, and to provide space for metabolic processes.

Bacteria vs. Archaea: Cell Walls, Membranes, Lipids, and Peptidoglycan

• Bacteria cell walls contain peptidoglycan, whereas archaea lack peptidoglycan and use pseudopeptidoglycan or other polysaccharides.
• Bacteria have phospholipid bilayers with ester-linked fatty acids in their cytoplasmic membranes, while archaea possess ether-linked isoprenoid chains that form bilayers or monolayers.
• Bacteria use ester-linked membrane lipids, in contrast to archaea, which use ether-linked lipids with branched chains.
• Peptidoglycan is present in bacteria, composed of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), but is absent in archaea, where pseudopeptidoglycan may take its place.

Functions of Bacterial Cell Membranes

• Bacterial cell membranes are selectively permeable, controlling substance passage into and out of the cell.
• These membranes are the site of ATP synthesis in aerobic bacteria for energy production.
• They facilitate nutrient and waste transport, crucial for maintaining cellular functions.
• Signal transduction occurs across these membranes, enabling detection of and response to environmental changes.
• Lastly, bacterial cell membranes are crucial in cell division, specifically forming the septum during binary fission.

Properties and Importance of Transport Proteins

• Transport proteins exhibit specificity for certain solutes, become saturated at maximum transport rates, and are subject to cellular regulation.
• These proteins are vital for nutrient uptake, waste removal, maintaining homeostasis via ion concentration regulation, and providing resistance to antibiotics and toxins.

Membrane Transporters: Energy, Modifications, and Protein Count

• Passive transport doesn't need energy, involving diffusion or facilitated diffusion.
• Active transport needs energy, such as ATP-driven pumps or proton motive force.
• Group translocation chemically alters the solute during transportation, like with the phosphotransferase system.
• Transporters can be uniporters (one solute), symporters (two solutes in the same direction), or antiporters (two solutes in opposite directions).

Necessity of Cell Walls and Survival Without

• Cell walls lend structural support, maintain cell shape, protect against osmotic pressure, prevent lysis in hypotonic environments.
• Bacteria like Mycoplasma survive without cell walls due to sterols in their membranes providing stability and living in osmotically stable habitats.

Bacterial Cell Membrane Proteins and Functions

• Transport proteins aid in moving substances across the membrane.
• Enzymes catalyze metabolic reactions.
• Receptors detect environmental signals to initiate responses.
• Adhesion proteins help cells attach to surfaces.
• Structural proteins maintain membrane integrity.

True vs. Pseudo Peptidoglycan

• True peptidoglycan, found in Bacteria, consists of NAG and NAM with peptide cross-links.
• Pseudopeptidoglycan, found in some Archaea, is composed of NAG and N-acetyltalosaminuronic acid (NAT) with unique peptide cross-links.

Cell Surface Structures, Inclusions, and Functions

• Capsules offer protection against desiccation and phagocytosis.
• S-layers serve as protective molecular sieves.
• Pili/Fimbriae facilitate attachment and conjugation.
• Storage granules store nutrients.
• Gas vesicles provide buoyancy.
• Magnetosomes aid in navigation.

Vegetative Cells vs. Endospores

• Vegetative cells are active but less resistant to harsh conditions.
• Endospores are dormant, highly resistant due to a thick coat, low water content, and high dipicolinic acid levels, enabling survival in extreme conditions.

Bacterial vs. Archaeal Flagella

• Bacterial flagella, made of flagellin protein, rotate like a propeller.
• Archaeal flagella consist of different proteins (archaellins), are thinner, and may rotate differently.

Bacterial Movement and External Stimuli

• Chemotaxis involves movement toward or away from chemicals.
• Phototaxis is movement in response to light.
• Aerotaxis is movement in response to oxygen.
• Magnetotaxis involves movement along magnetic fields.

Swimming vs. Gliding Motility

• Swimming involves flagella for rapid, directed movement in liquids.
• Gliding is flagella-independent, for slow, smooth movement on surfaces.

Gliding Motility Mechanisms

• Type IV pili are used by Myxococcus xanthus.
• Slime secretion is used by Cyanobacteria.
• Adhesion complexes are used by Flavobacterium.

Identifying Attractants and Repellents

• Chemotaxis assays observe bacterial movement in chemical gradients to identify attractants or repellents.
• Capillary assays measure bacterial accumulation in capillaries containing chemicals.

Forms of Bacterial Taxes

• Chemotaxis: Response to chemicals.
• Phototaxis: Response to light.
• Aerotaxis: Response to oxygen.
• Magnetotaxis: Response to magnetic fields.
• Thermotaxis: Response to temperature.

Peptidoglycan Synthesis

• Molecules involved: NAG and NAM form the glycan backbone; peptide cross-links provide structural integrity; Penicillin-binding proteins (PBPs) help with cross-linking.
• The synthesis process occurs in cytoplasm, membrane, and periplasmic space.
• This involves the formation of lipid II, which is then flipped to the outer side of the membrane for polymerization.

Bacterial Growth Cycle in Batch Culture

• Lag phase: Bacteria adapt to a new environment.
• Log phase: Rapid cell division.
• Stationary phase: Growth rate equals death rate, balancing the population.
• Death phase: Decline in viable cells due to depleted resources.
• These phases are affected by nutrient availability, temperature, pH, and oxygen levels.

Batch vs. Continuous Cultures

• Batch cultures are closed systems with no added nutrients post-inoculation.
• Continuous cultures are open, with constant nutrient addition and waste removal, maintaining a stable environment.

Microbial Adaptations to Temperature Extremes

• Psychrophiles have antifreeze proteins and unsaturated fatty acids to survive in cold conditions.
• Thermophiles have heat-stable enzymes, saturated fatty acids, and chaperonins to withstand high temperatures.

Compatible Solutes

• Compatible solutes are organic osmolytes protecting cells from osmotic stress, for example glycine betaine, proline, trehalose.

Bacteria Classifications by Growth Factors

• Temperature: Psychrophiles, mesophiles, thermophiles, hyperthermophiles.
• Oxygen: Aerobes, anaerobes, facultative anaerobes, microaerophiles.
• pH: Acidophiles, neutrophiles, alkaliphiles.
• Osmolarity: Halophiles, non-halophiles.

The "Great Plate Anomaly"

• The Great Plate Anomaly refers to the observation that most microorganisms in environmental samples cannot be cultured in laboratories.

Bacterial Quantification Methods

• Methods include plate counts, turbidity measurements, direct microscopic counts, and flow cytometry.
• Advantages/Disadvantages: vary in accuracy, speed, and suitability for different sample types.

Procedures for Quantification

• Plate counts: Serial dilution and plating, then count colonies.
• Turbidity: Measure optical density (OD) with a spectrophotometer.
• Direct counts: Use a hemocytometer or fluorescent dyes.

Factors Affecting Bacterial Growth

• Temperature: Affects enzyme activity and membrane fluidity.
• pH: Affects enzyme function and nutrient availability.
• Water availability: Affects osmotic balance.
• Oxygen: Determines metabolic pathways.

Molecular Adaptations to Temperature

• Psychrotrophs have antifreeze proteins and unsaturated membrane lipids for cold conditions.
• Thermophiles have heat-stable enzymes, saturated lipids, and chaperonins for hot conditions.

Aerobes vs. Anaerobes

• Aerobes use oxygen as a final electron acceptor in respiration.
• Anaerobes lack enzymes to detoxify reactive oxygen species (ROS).

Sterilization vs. Pasteurization

• Sterilization: Complete removal of all microbial life.
• Pasteurization: Reduces pathogens in heat-sensitive liquids.

Microbial Growth Control Methods

• Physical methods: Heat, radiation, filtration.
• Chemical methods: Disinfectants, antiseptics, antibiotics.
• Modes of action: Denature proteins, disrupt membranes, inhibit nucleic acid synthesis.

Sterilization Filters

• Membrane filters: Pore size 0.22 µm for bacteria.
• HEPA filters: For air sterilization.

Antimicrobial Susceptibility Assays

• Dilution method: Determine Minimum Inhibitory Concentration (MIC).
• Diffusion method: Measure zones of inhibition around antibiotic discs.

Determining MIC

• Serial dilutions of the compound are challenged against bacterial growth; the lowest concentration that inhibits growth is the MIC.

Antimicrobial Effects

• -static: Inhibits growth.
• -cidal: Kills cells.
• -lytic: Causes cell lysis.

Sterilant vs. Disinfectant vs. Antiseptic

• Sterilant: Kills all microbial life.
• Disinfectant: Reduces microbial load on surfaces.
• Antiseptic: Safe for use on living tissue.

Bacterial Nutritional Needs and Microbiological Media

• Requirements: Carbon, nitrogen, phosphorus, sulfur, trace elements.
• Media: Defined (exact composition known) and complex (exact composition unknown).

Microbiological Media Types

• Types: General-purpose, selective, differential, enrichment.
• Examples: Nutrient agar, MacConkey agar, Blood agar.

Cultivating Bacteria

• Solid media: Agar plates for colony isolation.
• Liquid media: Broths for bulk growth.

Aseptic Technique

• Aseptic technique: Prevents contamination.
• Importance: Ensures pure cultures for accurate study.

Energy Conservation Principles

• Principles: ATP generation, redox reactions.
• Classes: Phototrophs, chemotrophs, autotrophs, heterotrophs.

Microorganism Classification by Energy and Carbon

• Energy: Phototrophs (light), chemotrophs (chemicals).
• Carbon: Autotrophs (CO2), heterotrophs (organic compounds).

Redox Reactions in Energy Conservation

• Redox reactions: Transfer of electrons that release energy.

Enzyme Properties

• Properties: Specificity, catalytic efficiency, regulation.
• Enzymes catalyze redox reactions and facilitate energy transfer.

Energy Yield Factors

• Factors: Redox potential, efficiency of electron carriers.

Electron Carrier Importance

• Electron carriers shuttle electrons in metabolic pathways.

Energy Conservation Compounds

• Examples: ATP, GTP, phosphoenolpyruvate.
• Properties: Readily hydrolyzed high-energy bonds.

Phosphorylation

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP.
• Oxidative phosphorylation: The electron transport chain generates proton motive force.
• Photophosphorylation: Light drives electron transport.

Glycolysis and Citric Acid Cycle

• Glycolysis: Glucose to pyruvate, net gain of 2 ATP.
• Citric acid cycle: Acetyl-CoA to CO2, generates NADH, FADH2.

Fermentation Products

• Products: Lactate, ethanol, CO2.
• These regenerate NAD+ for glycolysis.

Fermentation vs. Respiration

• Fermentation occurs in anaerobic conditions or without terminal electron acceptors.

Electron Carriers in Respiration

• Order: NADH → Complex I → CoQ → Complex III → Cyt c → Complex IV → O2.
• The proton motive force is generated by proton pumping.

Proton Motive Force

• Sites: Complexes I, III, IV in the electron transport chain.

ATP Synthesis

• ATP synthase uses the proton gradient to phosphorylate ADP.

Citric Acid Cycle Functions

• Functions: Generates ATP and NADH/FADH2; also provides precursor molecules for biosynthesis.

CO2 Production

• Pathways: Glyoxylate cycle, reductive TCA cycle.

Bacteria Synthesis

• Synthesis: From central metabolic intermediates.
• Functions: Structural components, energy storage, genetic information.

Pentose Phosphate Pathway

• Generates NADPH and ribose-5-phosphate for biosynthesis.

Fatty Acid Synthesis

• Acetyl-CoA is elongated and reduced by fatty acid synthase.

Nitrogen Fixation Enzymes

• Enzymes: Nitrogenase complex (NifH, NifD, NifK).
• Function: Converts N2 to NH3.

Acetylene Reduction Assay

• Assay: Measures nitrogenase activity by conversion of acetylene to ethylene.
• Interpretation: Ethylene production rate indicates nitrogenase activity.

Photosynthesis Pigments

• Pigments: Chlorophylls, carotenoids, phycobilins.
• Functions: Light absorption, energy transfer.

Support for Different Phototrophs

• Coexistence: Different pigments absorb different wavelengths, lessening competition.

Calvin Cycle

• The calvin cycle includes Rubisco, phosphoglycerate kinase, G3P dehydrogenase.
• Functions: CO2 fixation, sugar synthesis.

Electron Flow

• Cyclic: Generates ATP only.
• Noncyclic: Generates ATP and NADPH.

CO2 Fixation Pathways

• Calvin cycle: CO2 fixation in plants and cyanobacteria.
• Reverse citric cycle: CO2 fixation in some bacteria.
• Hydroxypropionate pathway: CO2 fixation in green non-sulfur bacteria.

Photosynthetic Electron Flow

• Purple bacteria: Use bacteriochlorophylls, cyclic electron flow.
• Green sulfur bacteria: Use chlorosomes, noncyclic electron flow.
• Heliobacteria: Use bacteriochlorophyll g, cyclic electron flow.

Photosystems

• PSII: Splits water, generates oxygen.
• PSI: Reduces NADP+ to NADPH.

Anoxygenic Photosynthesis

• Conditions: Low oxygen and alternative electron donors.

Autotrophic Pathways

• Enzymes include Rubisco, ATP citrate lyase, and acetyl-CoA synthase. Reactions include CO2 fixation and acetyl-CoA formation.

Chemolithotrophy Energetics

• Energetics: Use of inorganic electron donors for energy.

Chemolithotrophs

• Include nitrifiers, sulfur oxidizers, and iron oxidizers.
• These vary in electron donors, carriers, and enzymes.

Fermentation Diversity

• Substrates: Glucose, amino acids, purines.
• Products: Lactate, ethanol, acetate, H2, CO2.

Anaerobic Respiration Processes

• Use of alternative electron acceptors (e.g., NO3-, Fe3+, SO42-, CO2).

Distinguishing Anaerobic Respiration

• Anaerobic respiration varies in electron carriers, enzymes, and acceptors.