Prokaryotes, and Archea 2020

Page 1: Introduction to Microbial World

• Focus: Prokaryotes (Bacteria & Archaea), Eukaryotes, and Viruses

• Course: MICR1010: Introductory Microbiology & Molecular Biology

Page 2: Classifying Living Things

• Biological Classification: Organisms grouped based on evolutionary relationships.

  • Evidence includes:

    • Fossil record

    • Comparative homologies (similarity in anatomy/physiology due to shared ancestry)

    • Comparative sequencing of Genetic Material (DNA & RNA)

Page 3: Gene Encoding and Phylogenetic Analysis

• Steps for analyzing rRNA genes:

  1. Isolate DNA from each organism.

  2. Make copies of rRNA gene by PCR.

  3. Sequence DNA.

  4. Analyze sequences and produce aligned rRNA gene sequences.

  5. Generate phylogenetic tree to show relationships between:

     • Archaea

     • Bacteria

     • Eukarya

• Examples of organisms include:

  • Green nonsulfur bacteria

  • Cyanobacteria

  • Various extremophiles (e.g., Methanogen)

Page 4: Three Domains of Life

• Bacteria: True bacteria, prokaryotic (e.g., Streptococcus pneumoniae, Lactobacillus).

• Archaea: Initially thought to be the same as bacteria, now identified as distinct prokaryotes (e.g., extremophiles).

• Eukarya: All eukaryotic organisms classified into four kingdoms:

  • Protista: Algae

  • Fungi: Mushrooms

  • Plantae: Ackee tree

  • Animalia: Humans

Page 5: Binomial Nomenclature

• System for Naming Organisms: Proposed by Carolus Linnaeus in 1700s.

  • Universal language: Latin

  • Each organism has:

    • Genus (capitalized)

    • Species (lower case)

  • Format: Names italicized or underlined

• Examples:

  • Vibrio cholerae

  • Homo sapiens

Page 6: Characteristics of Prokaryotes

• General Features:

  • Very small, single-celled, and relatively simple.

  • Genetic material not enclosed in a nuclear membrane.

  • Main shapes include bacillus (rod), coccus (sphere), and spiral (corkscrew).

Page 7: Bacterial Sizes

• Size range from 0.1 μm to 600 μm (visible).

  • Examples:

    • Mycoplasma: 100-200 nm diameter

    • Escherichia coli: 1.1-1.5 μm x 2-6 μm

    • Epulopiscium fishelsoni: up to 600 μm x 80 μm

Page 8: Surface-to-Volume Ratio

• Large surface-to-volume ratio enables efficiency.

• Microorganisms thrive despite simple morphologies due to minimal distance to surface.

Page 9: Bacterial Cell Morphology

• Cell shapes include:

  • Spherical (coccus)

  • Rod-shaped (bacillus)

  • Spiral-shaped

  • Comma-like, coiled forms

Page 10: Arrangement of Bacterial Cells

• Different planes of division result in:

  • Diplococci: in pairs

  • Streptococci: in chains

  • Tetrad: in groups of four

  • Sarcinae: cubical packets

  • Staphylococci: in clusters

Page 11: Arrangement of Bacilli

• Types include:

  • Diplobacilli: in pairs

  • Streptobacilli: in chains

  • Coccobacillus: short rod shape

Page 12: Spiral Bacteria Shapes

• Types include:

  • Vibrio: curved rod

  • Spirillum: spiral-shaped, rigid

  • Spirochete: flexible spiral

Page 13: Bacterial Shapes Summary

• Various patterns of cell arrangement and shape:

  • Diplo-, strepto-, staphylo- (e.g., cocci, bacilli, spirochetes)

Page 14: Prokaryotic Cell Structures

• External Structures:

  • Flagella, pili, fimbriae, glycocalyx (capsule/slime layer)

• Internal Structures:

  • Cytoplasmic matrix, ribosomes, nucleoid, inclusions, endospore

Page 15: Function of Prokaryotic Structures

• Plasma Membrane: Selectively permeable, boundary, transport, metabolism, environmental cue detection.

• Gas Vacuoles: Buoyancy in aquatic habitats.

• Ribosomes: Sites for protein synthesis.

• Nucleoid: Localization of genetic material.

Page 16: Overview of Prokaryotic Cells

• Basic structures include: Cell wall, plasma membrane, cytoplasm, nucleoid, and ribosomes.

• Variability in structures contributes to antibiotic targets and pathogenicity.

Page 17: Bacterial Cell Internal Composition

• Structures vary by species:

  • Capsule, cell wall, cytoplasmic membrane, nucleoid, ribosomes.

• Key roles in bacterial identification and antibiotic susceptibility.

Page 18: Gram-Positive vs. Gram-Negative Bacteria

• Gram-Positive Envelope:

  • Thick peptidoglycan layer with teichoic acids.

• Gram-Negative Envelope:

  • Thin peptidoglycan layer between inner and outer membranes.

  • Contains lipopolysaccharides (LPS).

Page 19: Structure of Bacterial Cell Walls

• Comparison of Gram-positive and Gram-negative cell envelopes, highlighting peptidoglycan and membrane structure.

Page 20: Characteristics of the Cell Wall

• Function:

  • Provides shape, protects from osmotic lysis, consists of peptidoglycan.

  • Teichoic acids present in Gram-positive bacteria; some bacteria lack a cell wall.

Page 21: Gram Staining Properties

• Gram-positive Example: Staphylococcus aureus

  • Staining process: crystal violet → Gram's iodine → decolorizer → safranin red.

• Gram-negative Example: Escherichia coli

Page 22: Features of Gram-Positive Cell Wall

• Peptidoglycan:

  • Thick layer making up most of the cell wall weight; contains teichoic and lipoteichoic acids.

Page 23: Components of Gram-Positive Cell Wall

• Structural features of Gram-positive bacteria include peptidoglycan and teichoic acid components.

Page 24: Peptidoglycan Structure

• Characteristics:

  • Mesh-like, thick structure composed of NAG and NAM repeating units with tetrapeptide chains regulating rigidity and support.

Page 25: Peptidoglycan Overview

• Description:

  • Three-dimensional latticework that surrounds and supports bacterium; critical for shape and protection.

Page 26: Gram-Negative Cell Wall Features

• Composition:

  • Outer membrane, thin peptidoglycan, and gel-like periplasmic space containing numerous proteins.

Page 27: Lipopolysaccharides in Gram-Negative Bacteria

• LPS Components:

  • Lipid A (toxic component), core, and O antigen (important for immune recognition).

Page 28: Importance of Gram-Negative LPS

• Functions include providing a permeability barrier, stabilizing the membrane, and eliciting immune responses.

Page 29: External Prokaryotic Structures

• Focus on flagella, fimbriae, and capsules as external features facilitating movement and adherence.

Page 30: Flagella Overview

• Structure: Thin (about 20 nm) and long, associated with motility.

• Types: Monotrichous, lophotrichous, amphitrichous, peritrichous.

Page 31: Arrangement of Flagella

• Visual representations of flagellar arrangements in bacteria:

  • Monotrichous, amphitrichous, lophotrichous, and peritrichous configurations.

Page 32: Bacterial Motility

• Types of movement initiated by:

  • Chemotaxis (chemical stimulus)

  • Phototaxis (light)

  • Aerotaxis (oxygen)

  • Magnetotaxis (magnetic field orientation)

Page 33: Bacterial Movement Patterns

• Behavior in response to attractants:

  • Random movement without attractants.

  • Directed movement toward attractants.

Page 34: Fimbriae and Pili Overview

• Fimbriae: Short, hair-like appendages aiding in attachment and biofilm formation.

• Pili: Longer structures facilitating adhesion, genetic exchange, and twitching motility.

Page 35: Fimbriae and Pili Functions

• Illustrate the roles of fimbriae and pili in bacterial adhesion and genetic transfer during conjugation.

Page 36: Glycocalyx Overview

• A sticky, gelatinous polymer external to the cell wall, composed of polysaccharides and/or polypeptides.

• Two main types:

  • Slime layer: loosely attached

  • Capsule: firmly attached, highly organized.

Page 37: Capsule Features

• Composed of varying polysaccharides, aiding in evasion of phagocytosis, adherence, virulence, and dehydration prevention.

Page 38: Internal Components of Prokaryotic Cells

• Structures include:

  • Cytoplasmic membrane, cytoplasm, ribosomes, nucleoid, inclusions, and endospores.

Page 39: Cytoplasmic Membrane Functions

• Apart from serving as a permeability barrier, plays roles in energy production and transport protein function.

Page 40: Cytoplasm as Antibiotic Target

• Key components include nucleoid, ribosomal subunits, plasmids.

• Targeted by different antibiotics to inhibit bacterial growth.

Page 41: Endospores in Bacteria

• Overview:

  • Dormant structures formed by certain Gram-positive bacteria to withstand harsh environmental conditions.

  • Subject to quick germination under favorable conditions.

Page 42: Endospore Formation Cycle

• Detailed stages of sporulation leading to endospore formation and subsequent germination under suitable conditions.

Page 43: Types of Endospores

• Classifications of endospores based on their terminal, subterminal, or central positioning within the bacterial cell.

Page 44: Gram-Negative vs. Gram-Positive Cell Walls

• Differences in peptidoglycan content, outer membrane presence, and susceptibility to antibiotics.

Page 45: Domain Archaea Overview

• Distinct from bacteria; found in extreme environments, lacking peptidoglycan but may contain pseudomurein.

Page 46: Archaea Characteristics

• Identified in late 1970s as unique domain; often live in extreme conditions and do not cause diseases in humans.

Page 47: Extremophiles Characteristics

• Require extreme environmental conditions including temperature, salinity, or pH.

• Subcategories include thermophiles, halophiles, and acidophiles.

Page 48: Halophiles and Thermophiles

• Definition:

  • Halophiles: thrive in saline environments.

  • Thermophiles: survive at elevated temperatures, such as those found in geothermal areas.

Page 49: Methanogens Overview

• Largest group of Archaea; produce methane as a metabolic byproduct found commonly in wetlands and guts of animals.

Page 50: Methane Cycle

• Details the ecological cycle involving methane production and oxidation, highlighting interactions between anaerobic environments and organism activity.

Page 51: Major Physiological Classes of Archaea

• Classes include extreme halophiles, thermoacidophiles, hyperthermophiles, and methanogens with examples provided.

Page 52: Unique Cellular Characteristics of Archaea

• Membrane lipids with ether-linked bonds and absence of peptidoglycan in cell walls.

Page 53: Archaeal Membranes

• Differences in membrane structure compared to bacteria and eukarya with ether bonds and lipid layers.

Page 54: Comparative Membrane Structure

• Contrast between membrane structures of Archaea, Bacteria, and Eukarya focusing on bonding types (ester vs ether).

Page 55: Habitats of Extreme Halophiles

• Various extreme environments showcasing organisms' adaptability to high salinity.

Page 56: Growth Conditions for Thermoplasma

• Thermoplasma habitat showing the importance of acidic, hot spring conditions for specific archaeal growth.

Page 57: Methanogen Overview

• Methanogens as strictly anaerobic organotrophs or chemoautotrophs prevalent in diverse environments.

Page 58: Comparative Summary of Cell Types

• Overview comparing Bacteria, Archaea, and Eukarya regarding structure, size, cell wall composition, and environmental habitats.