Microbiology Exam 2 Study Guide: Cell Structure, Metabolism, Growth, and Control

Cell Structure and Function

Cell Inclusions

Cell inclusions are specialized structures within microbial cells that serve as storage sites for nutrients and other important compounds. They help bacteria survive fluctuating environmental conditions by storing energy, carbon, phosphorus, and other elements.

• Polyphosphate granules: Store inorganic phosphate for nucleic acid and phospholipid synthesis.

• Sulfur granules: Accumulate elemental sulfur, often in periplasmic granules, which can be oxidized to sulfate.

• Carbon storage polymers:

  • Poly-β-hydroxybutyric acid (PHB): A lipid polymer synthesized when carbon is in excess; broken down as a carbon or energy source when needed.

  • Poly-β-hydroxyalkanoate (PHA): Similar to PHB, stores carbon monomers.

  • Glycogen: A glucose polymer serving as an energy reserve.

• Gas vesicles: Conical, gas-filled structures made of protein that confer buoyancy, allowing aquatic bacteria to position themselves optimally in the water column.

• Magnetosomes: Biomineralized magnetic iron oxides that allow bacteria to orient and migrate along magnetic field lines (magnetotaxis).

Endospores

Endospores are highly differentiated, dormant cells formed by certain Gram-positive bacteria (e.g., Bacillus and Clostridium) to survive unfavorable conditions.

• Structure: Multiple protective layers, contains dipicolinic acid (with Ca2+), and small acid-soluble spore proteins (SASPs) that protect DNA.

• Function: Resistant to heat, radiation, chemicals, drying, and nutrient deprivation.

• Life cycle: Vegetative cell → Endospore (sporulation) → Dormancy → Germination (activation, germination, outgrowth) → Vegetative cell.

• Staining: Special stains (e.g., malachite green with steam) are required to visualize endospores.

Flagella and Motility

Flagella are long, helical appendages that provide motility to many bacteria. Their arrangement and structure are key to understanding bacterial movement.

• Structure: Composed of flagellin protein (filament), hook, and basal body (motor).

• Arrangements: Polar (one or both ends), lophotrichous (tufts), amphitrichous (both ends), peritrichous (all over).

• Mechanism: Rotation powered by the proton motive force; speed and direction can be altered.

• Flagellar synthesis: Involves multiple genes; filament grows from the tip.

Surface Motility

• Twitching motility: Uses type IV pili to extend, attach, and retract, pulling the cell forward (e.g., Pseudomonas).

• Gliding motility: Smooth, continuous movement along the cell's long axis without external appendages (e.g., Myxococcus).

Chemotaxis

Chemotaxis is the directed movement of bacteria in response to chemical gradients.

• Run and tumble behavior: Alternating smooth runs (counterclockwise flagellar rotation) and tumbles (clockwise rotation) allow bacteria to change direction and move toward attractants or away from repellents.

• Chemoreceptors: Detect environmental signals and mediate movement.

• Other taxis: Phototaxis (light), osmotaxis (ionic strength).

Endosymbiotic Theory

The endosymbiotic theory explains the origin of mitochondria and chloroplasts as descendants of free-living bacteria engulfed by ancestral eukaryotic cells.

• Evidence:

  • Similar size to bacteria.

  • Own circular DNA.

  • 70S ribosomes (like prokaryotes).

  • Divide by binary fission.

  • Antibiotics affecting prokaryotic protein synthesis also affect these organelles.

• Modern examples: Symbiotic relationships in protists and termites.

Ribosomes

• Structure: Composed of RNA and protein; site of protein synthesis.

• Bacterial ribosomes: 70S (30S + 50S subunits), smaller than eukaryotic 80S ribosomes.

• Antibiotic target: Some antibiotics selectively inhibit 70S ribosomes.

Microbial Metabolism

Metabolism Overview

Metabolism encompasses all biochemical reactions in a cell, divided into catabolism (energy extraction) and anabolism (biosynthesis).

• Catabolism: Exergonic reactions that release energy, often conserved as ATP.

• Anabolism: Endergonic reactions that require energy for biosynthesis, using ATP and reducing power.

• ATP: The main energy currency, generated by substrate-level phosphorylation, oxidative phosphorylation, or photophosphorylation.

Free Energy and Redox Reactions

• Free energy change (ΔG0'): Indicates whether a reaction releases (exergonic, negative ΔG) or requires (endergonic, positive ΔG) energy.

• Redox reactions: Involve electron transfer from donor (oxidized) to acceptor (reduced).

• Reduction potential (E0'): Affinity of a substance for electrons; electrons flow from lower to higher reduction potential.

• Electron carriers: NAD+/NADH, NADP+/NADPH, quinones, cytochromes, and iron-sulfur proteins facilitate electron transfer.

Classification of Metabolic Types

• Phototrophs: Obtain energy from light (oxygenic or anoxygenic photosynthesis).

• Chemotrophs: Obtain energy from chemical compounds.

• Chemoorganotrophs: Use organic compounds for energy and electrons.

• Chemolithotrophs: Use inorganic compounds for energy and electrons.

• Autotrophs: Use CO2 as carbon source (primary producers).

• Heterotrophs: Use organic carbon sources.

Metabolic Pathways

• Glycolysis (Embden–Meyerhof–Parnas pathway): Universal pathway for glucose catabolism to pyruvate; net yield: 2 ATP, 2 NADH, 2 pyruvate per glucose.

• Pentose phosphate pathway: Generates NADPH (for biosynthesis) and ribose-5-phosphate (for nucleic acids).

• Entner-Doudoroff pathway: Alternative to glycolysis in some bacteria; net yield: 1 ATP, 1 NADH, 1 NADPH per glucose.

• Citric acid cycle (Krebs cycle): Oxidizes pyruvate to CO2; generates NADH, FADH2, and ATP.

Fermentation

• Definition: Anaerobic process where organic compounds serve as both electron donors and acceptors.

• Purpose: Regenerates NAD+ for glycolysis.

• Types: Lactic acid fermentation (e.g., Lactobacillus), alcoholic fermentation (e.g., yeast).

• Products: Lactic acid, ethanol, CO2, and other compounds.

Respiration and Electron Transport

• Aerobic respiration: Uses O2 as terminal electron acceptor; high ATP yield (up to 38 ATP per glucose).

• Anaerobic respiration: Uses alternative electron acceptors (e.g., nitrate, sulfate).

• Electron transport chain: Series of membrane-bound carriers that transfer electrons, generating a proton motive force (pmf).

• ATP synthase: Enzyme complex that uses pmf to synthesize ATP from ADP and Pi (oxidative phosphorylation).

Equation for ATP synthesis:

$\mathrm{ADP} + \mathrm{P_i} + \text{energy from pmf} \rightarrow \mathrm{ATP}$

Microbial Growth and Its Control

Nutritional Requirements

• Macronutrients: Required in large amounts (C, N, P, S, K, Mg, Ca, Fe).

• Micronutrients: Trace metals (e.g., Fe for respiration), growth factors (e.g., vitamins, amino acids, nucleotides).

Culture Media

• Defined media: Exact chemical composition known.

• Complex media: Contains digests of animal, plant, or microbial products.

• Selective media: Inhibits growth of some microbes, allows others.

• Differential media: Contains indicators to distinguish metabolic reactions.

• Solid media: Contains agar; allows observation of colony morphology.

Measuring Microbial Growth

• Microscopic cell count: Direct counting using a counting chamber.

• Spectrophotometry: Measures optical density (OD) at 540 nm; proportional to cell number but cannot distinguish live/dead cells.

• Serial dilution and plate count: Dilute sample, plate on agar, count colony-forming units (CFU).

• Viable count: Only counts living, reproducing cells.

Microbial Growth Cycle

• Binary fission: Cell division after cell enlargement; each daughter cell receives a chromosome and cell constituents.

• Batch culture: Closed system; growth curve has four phases:

  1. Lag phase: Adaptation, enzyme synthesis.

  2. Exponential (log) phase: Rapid, balanced growth; generation time calculated here.

  3. Stationary phase: Nutrient depletion/waste accumulation; growth rate zero.

  4. Death (decline) phase: Cell death exceeds growth.

• Continuous culture (chemostat): Fresh medium added, spent medium removed; maintains steady state.

Environmental Factors Affecting Growth

• Temperature: Microbes classified as psychrophiles (cold), mesophiles (moderate), thermophiles (hot), hyperthermophiles (very hot).

• pH: Each species has a specific pH range for growth (usually 3–9).

• Osmolarity: Water activity (aw) affects growth; high solute concentrations can inhibit growth.

• Oxygen requirements:

  • Obligate aerobes: Require O2.

  • Microaerophiles: Require reduced O2 levels.

  • Facultative anaerobes: Can grow with or without O2.

  • Obligate anaerobes: Killed by O2.

  • Aerotolerant anaerobes: Tolerate O2 but do not use it.

• Toxic oxygen species: Superoxide anion (O2-), hydrogen peroxide (H2O2), hydroxyl radical (OH-); destroyed by enzymes like superoxide dismutase and catalase.

Molecular Adaptations

• Cold adaptation: Enzymes with more α-helices, unsaturated fatty acids in membranes, cryoprotectants.

• Heat adaptation: Heat-stable proteins, saturated fatty acids, solutes stabilizing proteins (e.g., di-inositol phosphate).

Control of Microbial Growth

• Antimicrobial agents: Chemicals that kill (-cidal) or inhibit (-static) microbes.

• Types:

  • Sterilants: Destroy all microbes, including endospores.

  • Disinfectants: Kill most microbes, not necessarily endospores; used on surfaces.

  • Sanitizers: Reduce microbial numbers, less harsh.

  • Antiseptics: Kill/inhibit microbes, safe for living tissues.

• Assaying antimicrobial activity:

  • Minimum inhibitory concentration (MIC): Lowest concentration that inhibits growth.

  • Disk diffusion assay: Zone of inhibition around disk indicates effectiveness.

Glossary Table: Selected Key Terms

Term	Definition	Relevance/Example
CFU (colony-forming unit)	Unit used to estimate the number of viable bacteria or fungal cells in a sample	Used in plate counts to quantify living cells
Generation time	Time required for a microbial population to double in number	E. coli: ~20 minutes under optimal conditions
Chemoorganotroph	Organism that obtains energy and electrons from organic compounds	Most bacteria, fungi, and animals
Facultative anaerobe	Microbe that can grow with or without oxygen	Escherichia coli
Obligate anaerobe	Microbe that is killed by oxygen	Clostridium species
Oxidative phosphorylation	ATP synthesis using energy from electron transport and proton motive force	Occurs in aerobic and anaerobic respiration
Substrate-level phosphorylation	ATP synthesis by direct transfer of a phosphate group to ADP	Occurs in glycolysis and fermentation
Proton motive force	Electrochemical gradient of protons across a membrane	Drives ATP synthesis via ATP synthase
Batch culture	Closed-system culture with fixed volume and nutrients	Standard laboratory growth curve
Chemostat	Continuous culture device with constant addition/removal of medium	Maintains steady-state growth

Summary of Key Themes

• Energy Conservation and Transfer: Microbes use diverse metabolic pathways to conserve and transfer energy, primarily through ATP.

• Cellular Adaptations: Structures like flagella and endospores enable survival and motility in changing environments.

• Metabolic Diversity: Microbes exploit a wide range of energy, carbon, and electron sources, allowing them to inhabit diverse ecological niches.

• Environmental Influence: Growth and metabolism are shaped by temperature, pH, osmolarity, and oxygen availability.

• Experimental Tools: Techniques such as spectrophotometry, serial dilution, and plate counts are essential for studying microbial physiology.

• Growth Control: Chemical agents and environmental factors are used to control microbial growth in various settings.

Additional info: Some explanations and examples have been expanded for clarity and completeness based on standard microbiology textbooks.