BIOL 107 Microbiology Notes

Main Themes of Microbiology
- Study of organisms that cannot be seen without magnification.
- Etymology: “Micro” = Small; “Biology” = the study of living things.

Size and Visualization of Microorganisms

Microbiology definition
- The study of living things invisible to the unaided eye.
- Examples of sizes:
- Red blood cell: diameter 10{,}000\ \text{nm} in diameter
- Poliovirus: 30\ \text{nm}
- Bacteriophage MS2: 24\ \text{nm}
- Bacteriophage T4: 50\ \text{nm} \times 225\ \text{nm}
- Tobacco mosaic virus: 15\ \text{nm} \times 300\ \text{nm}
- E. coli (bacterium): 1000\ \text{nm} \times 3000\ \text{nm}
- Smallpox virus: 200\ \text{nm} \times 300\ \text{nm}
Smallest unaided visible size
- Approximately \approx 1\ \text{mm}
Size Range Activity (0.34 nm to 8 mm)
- Ranges from 0.34\ \text{nm} to 8\ \text{mm} in overall size

Microbes: Definitions, Roles, and Perceptions

Microbes (microorganisms)
- Dominant form of life on Earth in terms of numbers, biomass, and effects
- Includes Algae and Archaea
- Not to be confused with the colloquial term “germs.”
Public perception
- Tend to get bad press; many microbes are beneficial.
Medical microbiology focus
- Studies microbes that cause disease
- Only about 1\% of microbes cause disease

Positive Uses and Roles of Microbes

Food production
- Cheese, bread, beer
Medical and industrial applications
- Antibiotics, genetic engineering
Environmental and ecological roles
- Vital in aquatic food chains; water purification; nutrient cycles in soil
- Industrial waste removal; crucial for healthy human life

Cellular Organization: Prokaryotes vs Eukaryotes

Cell types
- Prokaryotic cells (e.g., Bacteria, Archaea)
- Eukaryotic cells (e.g., Fungi, Protozoa, Algae)
Key differences
- Prokaryotic:
- Smaller in size: 0.1\text{--}10\ \mu\text{m}
- DNA in one long strand (nucleoid), no nucleus
- No membrane-bound organelles
- Eukaryotic:
- Larger in size: 10\text{--}100\ \mu\text{m}
- DNA in chromosomes within a nucleus
- Has membrane-bound organelles

Similarities Between Prokaryotic and Eukaryotic Cells

Both contain:
- Nucleic acids: DNA/RNA (genetic material)
- Ribosomes (protein synthesis)
- Plasma membrane (controls movement in/out)

Kinds of Microorganisms

Bacteria
- Unicellular, prokaryotes; examples: Escherichia coli
- Visible only under microscope when isolated
Fungi
- Eukaryotic; can be multicellular or unicellular
Protozoa
- Unicellular, eukaryotes; note: term protozoa is broad and considered obsolete by some in Topic 2
Viruses
- Not composed of cells; intracellular parasites
- Replicate only inside a living cell
- All viruses have:
- Capsid (protein coat)
- Nucleic acid (DNA or RNA)
- Nucleocapsid = nucleic acid + protein coat
Virus details
- Some viruses have an envelope and spike proteins on the surface

Viruses: Survival, Life Status, and Replication

Survival outside the body
- Survival depends on the virus
- HIV: dies in seconds outside the body
- Flu virus: can live about 48\ \text{hours} outside the body
- General rule: viruses can reproduce only inside a host cell
Are viruses alive?
- They straddle the line of life
- They lack many internal structures/machinery essential for reproduction
- The criterion for life often cited: ability to move a genetic blueprint into future generations
- By this narrow criterion, viruses could be considered alive, but they typically are not considered living organisms outside a host

Visualization of Cells and Prokaryotes

Practice figure concept (Page 24)
- Prokaryotes lack a true nucleus; look for nucleolus, nuclear envelope, chromatin as indicators of eukaryotic cells
- Key features for prokaryotes: absence of nucleus, presence of nucleoid, simple internal structure

Measurement, Conversion, and Scientific Notation

Measuring microorganisms
- Use metric system (SI units)
Metric vs English system conversions
- 1 meter = 100 cm = 1000 mm
- 1 meter = 39.37 inches ≈ 3.28 feet
Metric system units and factors
- Meter: m, factor 1.0, decimal exponent 0
- Centimeter: \text{cm}, factor 10^{-2}, exponent -2
- Millimeter: \text{mm}, factor 10^{-3}, exponent -3
- Micrometer: \mu\text{m}, factor 10^{-6}, exponent -6
- Nanometer: \text{nm}, factor 10^{-9}, exponent -9
Conversions (examples)
- 5 cm to mm: 5\ \text{cm} \times \frac{10\ \text{mm}}{1\ \text{cm}} = 50\ \text{mm}
- 5\text{ mm} to cm: 5\ \text{mm} \times \frac{1\ \text{cm}}{10\ \text{mm}} = 0.5\ \text{cm}
Scientific notation
- Large numbers: 6{,}500{,}000 = 6.5 \times 10^{6}
- How to convert: move decimal to create a single-digit value between 1 and 9, count exponent places
- Small numbers: 1.65 \times 10^{6} mm, etc.
- For small numbers: 1.65 \times 10^{-6} m; exponent negative when moving decimal to the right
Practice notation exercises
- Examples: 652{,}000\ \mu\text{m} = 6.52 \times 10^{5}\ \mu\text{m}; 0.000917\ \text{m} = 9.17 \times 10^{-4}\ \, \text{m}

Naked Eye vs Microscopy and Object Sizes

Naked-eye visibility
- Typically limited to about 1\ \text{mm}; larger objects are visible without magnification
- Example: average human height ≈ 1.8\ \text{m} (for scale)
Visualizing objects smaller than the naked eye
- Light microscope: ~1\ ext{mm} to ~1\ \mu\text{m} range
- Amoeba: ~100\ \mu\text{m}
- Red blood cells: ~10\ \mu\text{m}
- Bacteria: ~1{-}10\ \mu\text{m}
Electron microscope: < 1\ \mu\text{m}
- DNA diameter: ~1\ \text{nm}
- HIV virus: ~100\ \text{nm}
- Flagellum: ~10\ \text{nm}

History: Visualization and Discovery of Microorganisms

Robert Hooke (1635–1703)
- Observed the first microbes (not bacteria) and published in Micrographia (1665)
- Introduced the name “cell”
Anton van Leeuwenhoek (1632–1723)
- Considered the first microbiologist
- First to see and describe bacteria using high-quality single-lens microscopes (300–500x)
- Referred to organisms as "animalcules"

Abiogenesis, Biogenesis, and Germ Theory

Abiogenesis (spontaneous generation)
- Pre-mid 1800s belief that living organisms arise from nonliving matter (e.g., maggots from meat, mice from grain)
Key experiments against abiogenesis
- Francesco Redi (late 1600s): controlled experiments showing maggots come from flies, not meat
- Lazzaro Spallanzani (late 1700s): boiled broth; no microbial growth in sealed containers; argued microbes come from air
- Louis Pasteur (mid- to late 1800s): swan-neck flask experiments preventing contamination; broth remains sterile without exposure to air.
Theory of biogenesis
- Pasteur’s conclusion: living things come from other living things; life arises from parents, not spontaneously
Pasteurization
- Heating wine to prevent souring microbial growth; established germ theory of disease
- Germ theory: microorganisms cause disease

Recent and Ongoing Discoveries in Microbiology

Electron microscopy advancements
- Allowed viewing of viruses and cellular components in greater detail
Vaccinations (covered more in Topic 19)
Genomic sequencing and bioengineering
- Rise of modern genomics and synthetic biology applications

Quick Practice and Concepts Review (Key Takeaways)

The four microbes typically studied in basic microbiology include Bacteria, Fungi, Protozoa, and Viruses.
Prokaryotes vs. Eukaryotes: structural differences (nucleus, organelles) and size ranges; plan for recognizing features.
Viruses are not cells and require a host to replicate; some have envelopes and spike proteins; survival outside host varies greatly by virus.
The historical shift from abiogenesis to biogenesis was driven by Redi, Spallanzani, and Pasteur; Pasteur’s experiments supported germ theory and biogenesis.
Measurement skills are essential: metric system, dimensional analysis, and scientific notation for communicating microbial scales.
Visualization scales: naked-eye (~1 mm), light microscopy (μm range), and electron microscopy (nm range).
Practical applications of microbes include food production, medicine (antibiotics, vaccines), environmental roles (recycling nutrients, water purification), and biotechnological advances.
Ethical and practical implications: reliance on microbes for health and industry versus responsible handling and safe practices in biotechnology.