LECTURE 1 and 2 Flashcards
(29 cards)
What is the main DNA store in bacteria
The Nucleoid
Definition: the irregular-shaped region within a bacterial cell that contains the main genomic DNA.
Copy number: Typically one per cell
Why not visible by light microscopy?
DNA is tightly coiled and compacted due to its length (~1 mm long in E. coli).
Coiled via supercoiling and DNA-binding proteins (like HU, IHF) to fit into the small cytoplasm.
Function: Contains all genes necessary for essential cellular functions.
Plasmids – Bacterial ‘Superpowers’
Definition: Small circular DNA molecules, separate from the nucleoid, often non-essential.
Replication: Independently replicating (autonomously).
Copy number: Varies by plasmid type:
High-copy → multiple copies, more likely passed to daughter cells, but burdens the cell metabolically.
Low-copy → fewer copies, less metabolic load but lower inheritance reliability.
‘Superpower’ genes: Can carry genes for antibiotic resistance, virulence, heavy metal resistance.
Bacterial Storage and Survival Structures: Inclusions
Definition: Storage granules that accumulate under nutrient-limiting conditions (usually stationary phase).
Function: Store energy and nutrients to help bacteria survive during starvation.
Bacterial Storage and Survival Structures - Major stored elements
Carbon: Stored as:
Glycogen: Slow-release, compact glucose polymer; suits slow-metabolising stationary-phase cells.
Polyhydroxybutyrate (PHB): Biodegradable polymer; of interest in sustainable plastic production.
Phosphorus: Stored in polyphosphate granules.
Sulfur: Stored in sulfur granules (used in respiration or amino acid synthesis).
Cell Envelope Structures: Plasma Membrane
Structure: Phospholipid bilayer with integral and peripheral proteins.
Function: Selective barrier, site of respiration and ATP generation (no mitochondria in bacteria).
Cell Envelope Structures: Cell Wall
Purpose: Maintains shape, prevents osmotic lysis.
Peptidoglycan: Polymer of N-acetylglucosamine (G) and N-acetylmuramic acid (M) with crosslinked peptide bridges.
Cell Wall – Gram Stain Types: Gram-Positive
Thick peptidoglycan layer (~90%).
Teichoic and lipoteichoic acids:
Aid in wall rigidity and immune interactions (e.g., binding phagocyte receptors).
Cell Wall – Gram Stain Types: Gram-negative
Thin peptidoglycan (~10%).
Surface Layers and Motility Structures: Capsule
Composition: Polysaccharides.
Function:
Anti-phagocytic shield.
Hides antigens.
Helps surface adhesion and biofilm formation.
Surface Layers and Motility Structures: S-layer
S-layer (Surface-layer)
Made of glycoproteins.
Found in: All Archaea, some Bacteria.
Function: Structural support, immune evasion, adhesion
Surface Layers and Motility Structures: Flagella
Structure: Motor-driven protein filaments.
Types based on location:
Function: Swimming motility via rotation (powered by proton motive force).
Surface Layers and Motility Structures: Fimbriae vs Pili
Fimbriae:
Short, numerous (~1000/cell).
Function: Surface adhesion, biofilm formation.
Pili:
Longer, fewer (1–10/cell).
Function: DNA transfer (conjugation), host cell attachment.
Ribosomes and Molecular Phylogeny: 70S Ribosome
Subunits:
50S: 5S rRNA, 23S rRNA, 34 proteins.
30S: 16S rRNA, 21 proteins.
Why is 16S rRNA important?
Highly conserved, but contains hypervariable regions.
Used to construct phylogenetic trees by sequence comparison.
Basis of classification of Archaea, Bacteria, Asgard (a new superphylum).
Bacterial Classification and Identification: Taxonomy Hierarchy
Order: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species → Strain.
Biosafety Levels
Class 1: Harmless (e.g., Lactobacillus).
Class 2: Mildly pathogenic (e.g., E. coli).
Class 3: Pathogenic, treatable (e.g., Mycobacterium tuberculosis).
Class 4: Pathogenic, no known treatment (e.g., Ebola, but rare in bacteria).
Differential Media
Definition: Allow multiple microbes to grow but show phenotypic differences.
Differential Media: MacConkey agar
Grows Gram-negatives.
Contains lactose and pH indicator.
Lactose fermenters (e.g. E. coli) → pink.
Non-fermenters → colorless.
Differential Media: Blood Agar
β-hemolysis: Complete RBC lysis (e.g. S. pyogenes).
α-hemolysis: Partial RBC lysis (e.g. E. coli).
γ-hemolysis: No RBC breakdown.
Differential Media: Chocolate Agar
Boiled blood agar.
Grows fastidious organisms like Haemophilus and Neisseria.
Problem: Non-selective; both can grow.
Selective Media
Contain inhibitors that suppress all but one genus or species.
Example: Mannitol salt agar (selects Staphylococcus).
High salt inhibits most organisms.
Mannitol fermentation → color change (e.g. S. aureus = yellow).
Classical Tests: Gram staining
Purpose: To classify bacteria based on their cell wall structure (peptidoglycan thickness).
Process:
Apply crystal violet (primary stain) → stains all bacteria purple.
Add iodine (mordant) → forms CV-I complex.
Use alcohol or acetone (decolorizer).
Gram-positive retain purple (thick peptidoglycan traps stain).
Gram-negative lose the purple (thin peptidoglycan can’t retain it).
Counterstain with safranin → Gram-negative appear pink/red.
Result:
Gram-positive: purple.
Gram-negative: pink/red
Classical tests: Morphology
Shapes:
Cocci (spherical)
Bacilli (rod-shaped)
Spirilla (spiral-shaped)
Arrangements:
Streptococci (chains)
Staphylococci (clusters, like grapes)
Diplococci (pairs)
Palisades (side-by-side rods)
Classical tests: Oxygen Tolerance Testing
How: Inoculate bacteria into thioglycollate medium or soft agar tube.
Results:
Obligate aerobes: grow only at top (need oxygen).
Obligate anaerobes: grow at bottom (oxygen is toxic).
Facultative anaerobes: grow throughout, but denser at top (prefer oxygen).
Aerotolerant anaerobes: grow evenly; oxygen doesn’t affect them.
Microaerophiles: grow just below the top (need low O₂).
Classical tests: Catalase Test
Purpose: Detects catalase enzyme (breaks down H₂O₂ → H₂O + O₂).
How: Place a drop of hydrogen peroxide on a bacterial smear.
Positive: bubbling (e.g., Staphylococcus spp.)
Negative: no bubbling (e.g., Streptococcus spp.)
Clinical use: Differentiates Gram-positive cocci.
