Microbiology Study Guide: Domains of Life, Bacterial Cell Structure, and Growth

Three Domains of Cellular Life

Overview of Archaea, Bacteria, and Eukarya

The three domains of life—Archaea, Bacteria, and Eukarya—represent fundamental divisions based on cellular structure, genetics, and biochemistry.

• Archaea: Prokaryotic cells, unique membrane lipids, often extremophiles, lack peptidoglycan in cell walls.

• Bacteria: Prokaryotic cells, peptidoglycan cell walls, diverse metabolic pathways, found in many environments.

• Eukarya: Eukaryotic cells, membrane-bound organelles, includes plants, animals, fungi, and protists.

Similarities and Differences:

• Archaea & Bacteria: Both are prokaryotes, lack nucleus, reproduce by binary fission.

• Archaea & Eukarya: Share some genetic and metabolic pathways, similar RNA polymerase.

• Bacteria & Eukarya: Both can have similar metabolic processes, but differ in cell structure.

Organisms Included: Archaea (e.g., Halobacterium), Bacteria (e.g., Escherichia coli), Eukarya (e.g., Homo sapiens, Saccharomyces cerevisiae).

Evidence for Evolution & Horizontal Gene Transfer

• Evolution: Supported by molecular comparisons, fossil evidence (e.g., stromatolites), and phylogenetic trees.

• Horizontal Gene Transfer (HGT): Movement of genetic material between organisms, mechanisms include conjugation, transformation, and transduction.

• Conjugation: Direct transfer of DNA via pilus.

Phylogenetic Tree Dynamics & Endosymbiosis

• Nature of Chloroplasts: Originated from cyanobacteria via endosymbiosis.

• Endosymbiont Theory: Eukaryotic organelles (mitochondria, chloroplasts) evolved from prokaryotic cells engulfed by ancestors of eukaryotes.

Key Characteristics of the Three Domains

• rRNA Alignment & Signature Sequences: Used to classify organisms; 16S rRNA for prokaryotes, 18S rRNA for eukaryotes.

• Ribosomal Size: Bacteria/Archaea: 70S; Eukarya: 80S.

• Compartmentalization: Eukarya have internal membranes and organelles; prokaryotes lack these.

• Genome: Bacteria/Archaea: circular DNA; Eukarya: linear chromosomes.

• Plasmids: Extra-chromosomal DNA, common in bacteria and archaea.

• Molecular Genetics: Differences in polymerases, tRNAs, presence of introns (mainly in eukaryotes).

• Resistance & Sensitivity: Varies by domain; e.g., antibiotics affect bacteria, not archaea.

• Biochemistry: Nitrogen fixation (e.g., Rhizobium), methanogenesis (unique to archaea).

• ATP Synthase: Present in all domains, mechanism varies.

• Cell Wall: Bacteria: peptidoglycan; Archaea: pseudopeptidoglycan; Eukarya: cellulose/chitin (if present).

• Membrane Lipids: Bacteria/Eukarya: ester-linked; Archaea: ether-linked.

• Chemolithotrophy: Energy from inorganic compounds, common in bacteria and archaea.

• Chlorophyll-Based Photosynthesis: Cyanobacteria, plants, algae.

• Environmental Niches: Archaea often extremophiles; bacteria and eukarya occupy diverse habitats.

Names to Remember

• Carl Woese: Defined the three domains using rRNA sequencing.

• Leeuwenhoek: First to observe microbes.

• Pasteur, Lister, Koch: Pioneers in microbiology and germ theory.

• Koch's Postulates: Criteria to establish causative relationship between microbe and disease.

Early Life & Evolution of Cells

• Cyanobacteria: Early photosynthetic bacteria, contributed to oxygenation of atmosphere.

• Stromatolites: Fossilized microbial mats, evidence of early life.

• RNA World Hypothesis: RNA may have been the original genetic material due to its catalytic properties.

• Acellular Forms: Viroids, viruses, prions—lack cellular structure, unique replication mechanisms.

Bacterial Cell Structure and Morphology

Cellular Morphology & Types

Bacterial cells exhibit diverse shapes and arrangements, which influence their ecological roles and identification.

• Cocci: Spherical cells (e.g., Staphylococcus).

• Bacilli: Rod-shaped cells (e.g., Escherichia coli).

• Coccobacilli: Short rods, intermediate between cocci and bacilli.

• Vibrios: Curved rods (e.g., Vibrio cholerae).

• Spirilla: Spiral-shaped, rigid.

• Spirochetes: Flexible, spiral-shaped (e.g., Treponema).

• Myxobacteria, Actinomycetes: Complex multicellular structures.

Cell Size and Shape: Determined by genetic, environmental, and structural factors; affects nutrient uptake and motility.

Comparison of Bacterial, Plant, and Animal Cells

• Bacterial Cells: Prokaryotic, lack nucleus, cell wall (peptidoglycan), small size (0.5–5 μm).

• Plant Cells: Eukaryotic, nucleus, cell wall (cellulose), chloroplasts.

• Animal Cells: Eukaryotic, nucleus, no cell wall, larger size.

Bacterial Cell Walls

Gram Positive vs. Gram Negative Cell Walls

Bacterial cell walls are classified based on their structure and staining properties.

• Gram Positive: Thick peptidoglycan layer, teichoic acids, no outer membrane.

• Gram Negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS), periplasmic space.

Peptidoglycan Structure

• N-Acetyl Muramic Acid (NAM) and N-Acetyl Glucosamine (NAG): Alternating sugars forming backbone.

• Peptide Interbridges: Cross-linking peptides for strength.

Other Cell Wall Components

• Teichoic Acid & Lipoteichoic Acid: Found in gram-positive walls, contribute to rigidity and ion transport.

• Braun’s Lipoprotein: Anchors outer membrane to peptidoglycan in gram-negative bacteria.

• Lipopolysaccharide (LPS): Outer membrane component, includes Lipid A (endotoxin), core polysaccharide, O antigen.

• Porins: Channels for molecule transport in gram-negative bacteria.

• Mycolic Acid: Waxy layer in acid-fast bacteria (e.g., Mycobacterium).

Outer Coverings

• Capsules: Polysaccharide layer, protects against desiccation and phagocytosis.

• S-layers: Protein layers, structural support.

• Slime Layers: Loosely attached, aids in gliding motility.

• Glycocalyx: General term for extracellular polysaccharide matrix.

Motility Structures

Flagella: Structure and Function

• Structure: Basal body (rings), hook, filament.

• Ring Differences: Gram-positive: fewer rings; gram-negative: more complex.

• MotA and MotB: Proteins involved in motor function.

• Proton Motive Force: Drives flagellar rotation.

• Types of Flagella Placement: Monotrichous (single), peritrichous (multiple), lophotrichous (tufts).

• Swarming: Coordinated movement across surfaces.

• Rotation: Counterclockwise (CCW) = run; clockwise (CW) = tumble.

Axial Filaments & Spirochetes

• Axial Filaments: Internal flagella in spirochetes, enable corkscrew motion.

• Periplasmic Sheath: Surrounds axial filaments.

Fimbriae and Pili

• Fimbriae: Short, numerous, for attachment.

• Pili: Longer, fewer, involved in adhesion, invasion, colonization, and movement (twitching).

Bacterial Genome and Plasmids

Genome Structure

• Chromosome: Usually circular, contains essential genes.

• Plasmids: Small, circular DNA, carry non-essential genes (e.g., antibiotic resistance).

Cell Membrane and Transport Processes

Fluid Mosaic Model

• Structure: Phospholipid bilayer with embedded proteins, dynamic and flexible.

Movement Across Membranes

• Passive Diffusion: Movement down concentration gradient, no energy required.

• Facilitated Diffusion: Uses transport proteins.

• Active Transport: Requires energy (ATP or ion gradients).

• Primary Active Transport: ATP Binding Cassette (ABC) transporters.

• Secondary Active Transport: Major Facilitator Superfamily (MFS) transporters, driven by ion gradients.

• Proton Motive Force: $\Delta p = \Delta \Psi - (2.3RT/F) \Delta pH$

• Ion Gradients: Na+ and K+ gradients used for transport.

Movement Across Cell Walls

• Aquaporins: Water channels.

• Porins: Allow passage of small molecules in gram-negative and acid-fast cell walls.

• ATP Binding Cassette: Complex of binding protein, transmembrane domain, cytoplasmic domain, ATP hydrolysis.

• PTS (Phosphotransferase System): Group translocation, transfers phosphate to sugars during transport.

Chemotaxis and Motility

• Chemotaxis: Movement toward or away from chemical stimuli, involves flagellar rotation and signal transduction.

• Motility Types: Flagellar movement, twitching (pili), gliding (slime layer).

Bacterial Growth

Reproductive Strategies

• Binary Fission: Most common, cell divides into two identical cells.

• Other Methods: Budding, fragmentation.

Bacterial Cell Cycle

• Three Cell Cycles: DNA replication, cell growth, division.

• Comparison to Eukaryotes: No mitosis/meiosis, simpler regulation.

DNA Replication Vocabulary

• Lagging Strand: Synthesized discontinuously.

• Leading Strand: Synthesized continuously.

• 3'-5': Directionality of DNA strands.

• Topoisomerase: Relieves supercoiling.

• Helicase: Unwinds DNA.

• Replication Fork: Site of active replication.

• Single Strand Binding Proteins: Stabilize unwound DNA.

• DNA Polymerase III: Main enzyme for synthesis.

• DNA Polymerase I: Removes primers, fills gaps.

• Primer: Short RNA sequence for initiation.

• Exonuclease Activity: Removes nucleotides.

• Ligase: Joins Okazaki fragments.

• Okazaki Fragments: Short DNA segments on lagging strand.

Microbial Growth Curves

• Phases: Lag, log (exponential), stationary, death.

• Importance: Understanding growth helps in controlling infections, optimizing industrial processes.

Factors Influencing Microbial Growth

• Osmosis: Water movement affects cell integrity.

• Mechanosensitive Channels: Protect against osmotic stress.

• Halophiles: Thrive in high salt; e.g., Halobacterium.

• Acidophiles: Grow in low pH; e.g., Acidithiobacillus.

• Neutrophiles: Prefer neutral pH.

• Alkaliphiles: Grow in high pH; e.g., Bacillus alcalophilus.

• Temperature Adaptation: Psychrophiles (cold), mesophiles (moderate), thermophiles (hot).

• Starvation Adaptation: Formation of persisters, biofilms.

Biofilms and Quorum Sensing

• Biofilm: Community of microbes attached to surface, embedded in extracellular matrix.

• Formation: Attachment, growth, maturation, dispersal.

• Importance: Medical relevance (e.g., chronic infections, device contamination).

• Quorum Sensing: Cell-to-cell communication via signaling molecules (e.g., N-acyl homoserine lactone, AHL).

• Cross-Species Communication: Example: Rhizobium in plant root nodules.

Media Types

• General Purpose Media: Supports growth of many microbes.

• Selective Media: Favors growth of specific microbes.

• Differential Media: Distinguishes microbes based on biochemical properties.

Vocabulary and Key Concepts

• Oligotrophic Environment: Low nutrient availability.

• Growth Arrest: Temporary cessation of cell division.

• Extracellular Polymeric Substance: Matrix in biofilms.

• Persisters: Dormant cells resistant to stress.

• Competent State: Ability to take up DNA from environment.

Table: Comparison of Gram Positive and Gram Negative Cell Walls

Feature	Gram Positive	Gram Negative
Peptidoglycan Layer	Thick	Thin
Teichoic Acids	Present	Absent
Outer Membrane	Absent	Present
Lipopolysaccharide (LPS)	Absent	Present
Periplasmic Space	Small/None	Large
Staining	Purple	Pink

Example: Quorum Sensing in Vibrio fischeri

• Mechanism: Bacteria produce AHL, which accumulates and triggers gene expression for bioluminescence when threshold is reached.

Additional info: Academic context was added to expand brief points and clarify terminology, as original notes were fragmented and listed concepts without full explanations.