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BIO205: EXAM PREP CHAP 1

1. Understanding Microbes
1.1 Microbe Shapes and Life Cycles

  • Shapes (Morphology):

    • Cocci: Spherical (e.g., Streptococcus pneumoniae)

    • Bacilli: Rod-shaped (e.g., Bacillus cereus)

    • Spirilla/Spirochetes: Spiral-shaped

    • Vibrios: Comma-shaped

  • Life Cycles: Many microbes have complex life cycles involving different stages of growth, reproduction, and survival strategies.

    • Bacterial Endospores: Dormant, highly resistant structures formed by some bacteria (e.g., Bacillus, Clostridium) for survival under harsh conditions.

    • Fungal Budding: Asexual reproduction in yeasts (e.g., Saccharomyces cerevisiae) where a new organism develops from an outgrowth or bud due to cell division at one particular site.

    • Parasitic Life Cycles: Often involve multiple hosts and stages (e.g., Plasmodium falciparum involves human and mosquito hosts, with different forms in each).

1.2 Major Differences between Bacteria, Archaea, and Eukarya

  • Bacteria:

    • Cell Type: Prokaryotic

    • Cell Wall: Contains peptidoglycan

    • Membrane Lipids: Ester-linked fatty acids

    • Ribosomal RNA (rRNA): Unique sequences

    • Histones: Absent

    • Environment: Diverse environments, including human pathogens

  • Archaea:

    • Cell Type: Prokaryotic

    • Cell Wall: Lacks peptidoglycan (contains pseudopeptidoglycan or S-layers)

    • Membrane Lipids: Ether-linked branched hydrocarbons

    • Ribosomal RNA (rRNA): Unique sequences, more similar to Eukarya than Bacteria

    • Histones: Present in some species, associated with DNA

    • Environment: Often extremophiles (e.g., halophiles, thermophiles, methanogens like Methanobrevibacter smithii)

  • Eukarya:

    • Cell Type: Eukaryotic

    • Cell Wall: Variable (absent in animals, chitin in fungi, cellulose in plants); never peptidoglycan

    • Membrane Lipids: Ester-linked fatty acids

    • Ribosomal RNA (rRNA): Unique sequences, distinct from Bacteria and Archaea

    • Histones: Present, associated with DNA in chromosomes

    • Organelles: Membrane-bound organelles (nucleus, mitochondria, chloroplasts, etc.)

    • Reproduction: Sexual and asexual

    • Size: Generally larger than prokaryotes

2. Historical Experiments Shaping Modern Microbiology
2.1 Pasteur's Swan-Neck Flask Experiment

  • Disproved Spontaneous Generation: Louis Pasteur's experiment definitively showed that life arises from pre-existing life, not spontaneously from non-living matter.

  • Experiment Design:

    1. He used flasks with long, S-shaped (swan) necks.

    2. He boiled broth in these flasks to sterilize them, killing any existing microbes.

    3. The S-shaped neck allowed air to enter but trapped airborne dust particles and microbes in the bend.

    4. The broth remained sterile indefinitely because microbes could not reach it.

    5. If the neck was broken or the broth was tilted into the neck, the broth became contaminated as microbes from the air could now enter.

  • Conclusion: Microbes in the air, not spontaneous generation, caused spoilage.

2.2 Development of Sterile Technique from Germ Theory

  • Germ Theory of Disease: Proposed that microorganisms cause many diseases. This concept, championed by Pasteur and Robert Koch, provided the foundation.

  • Sterile Technique (Aseptic Technique):

    • Origin: The understanding that invisible microbes cause disease led to practices designed to prevent contamination by these microbes.

    • Pioneers: Joseph Lister applied germ theory to surgical practices, using carbolic acid to sterilize instruments and wounds, significantly reducing post-surgical infections.

    • Principles: Involves methods to prevent contamination by unwanted microorganisms, such as:

      • Sterilization of instruments and media (heat, chemicals, filtration).

      • Disinfection of surfaces.

      • Aseptic handling (working near a flame, wearing gloves, masks).

    • Impact: Crucial for modern medicine, surgery, and microbiological research, ensuring accurate results and patient safety.

3. Microbial Taxonomy and Phylogeny
3.1 Basic Structure of Taxonomy

  • Taxonomy: The science of classifying organisms. It involves:

    • Classification: Arranging organisms into groups based on similarities.

    • Nomenclature: Assigning names to these groups.

    • Identification: Determining an organism's identity.

  • Hierarchical Order: A nested hierarchy from broad to specific:

    • Domain

    • Kingdom

    • Phylum

    • Class

    • Order

    • Family

    • Genus

    • Species

3.2 Binomial Nomenclature

  • System: Developed by Carl Linnaeus.

  • Naming Convention: Each organism is given a two-part scientific name:

    • The first part is the Genus (always capitalized).

    • The second part is the species epithet (always lowercase).

    • Both parts are italicized (e.g., Escherichia coli, Homo sapiens).

  • Purpose: Provides a universal, unambiguous name for each organism, facilitating clear scientific communication.

3.3 Modern Three-Domain System

  • Concept: A biological classification introduced by Carl Woese in 1977, based on ribosomal RNA (rRNA) gene sequencing.

  • Domains: Divides all cellular life into three major domains:

    1. Bacteria: (True bacteria)

    2. Archaea: (Ancient bacteria, often extremophiles)

    3. Eukarya: (All organisms with eukaryotic cells: protists, fungi, plants, animals)

  • Why rRNA is Used for Phylogenetic Analysis:

    • Ubiquitous: Present in all cellular organisms because it is essential for protein synthesis.

    • Conserved Regions: Contains regions that are highly conserved across diverse species, allowing for alignment and comparison.

    • Variable Regions: Also contains variable regions that show differences between species, allowing for phylogenetic discrimination.

    • Slow Rate of Evolution: Its critical role means that rRNA genes evolve slowly, making them excellent molecular chronometers for tracking evolutionary relationships over long periods.

4. Examples of Key Organisms and Their Features

  • Plasmodium falciparum:

    • Type: Protozoan parasite.

    • Disease: Causes the most severe form of malaria.

    • Life Cycle: Complex, involving two hosts (human and Anopheles mosquito).

    • Features: Infects human red blood cells, leading to cyclical fever and chills; can cause cerebral malaria.

  • Saccharomyces cerevisiae:

    • Type: Eukaryotic fungus (yeast).

    • Common Name: Baker's yeast or brewer's yeast.

    • Features: Facultative anaerobe; used in baking (leavening bread through CO_2 production) and brewing (alcohol fermentation);

  • Bacillus cereus:

    • Type: Gram-positive, rod-shaped bacterium.

    • Features: Spore-forming (can survive harsh conditions); common in soil and food; can cause food poisoning (emetic toxins causing vomiting, diarrheal toxins causing diarrhea).

  • Streptococcus pneumoniae:

    • Type: Gram-positive, spherical (cocci) bacterium, typically arranged in pairs or chains.

    • Disease: Major cause of pneumonia, otitis media (middle ear infection), meningitis, and septicemia.

    • Features: Possesses a polysaccharide capsule that helps it evade the host immune system; part of the normal flora of the upper respiratory tract.

  • Methanobrevibacter smithii:

    • Type: Anaerobic Archaea (specifically, a methanogen).

    • Habitat: Prominent member of the human gut microbiota.

    • Features: Produces methane (CH_4) as a metabolic byproduct, contributing to intestinal gas and potentially influencing host metabolism and obesity.