MICROBIO TOPIC 1 CH1-3 GCU

microbiology

Microbiology is the science born in 1674 with van Leeuwenhoek’s discovery of “animalcules,” focusing on organisms too small to be seen without a microscope. Microbiology is the study of microorganisms, including bacteria, archaea, fungi, protozoa, algae, and acellular infectious agents (viruses, viroids, prions).

microorganism

A microorganism is an organism too small to be seen with the unaided eye, including bacteria, archaea, many eukaryotes (fungi, algae, protozoa), and acellular agents.

why microorganisms have been successful

• High surface-area-to-volume ratio → rapid nutrient uptake

• Rapid growth

• Survival in extreme environments (extremophiles)

• Occupy every environment (ubiquitous)

• Perform essential processes (nitrogen fixation, oxygen production, decomposition)

diversity of microorganisms

• Three domains: Bacteria, Archaea, Eukarya

• Acellular agents: viruses, viroids, prions

• Enormous variation in size, shape, metabolism, and habitat

• Microbes outnumber mammals by 10,000×

• Less than 1% can be cultured

• Found in all environments

types of organisms encountered in microbiology

• Prokaryotes (Bacteria, Archaea)

• Eukaryotes (Fungi, Algae, Protozoa, Helminths)

• Acellular agents (Viruses, Viroids, Prions)

important roles of microorganisms

• Recycling nutrients

• Oxygen production

• Nitrogen cycle

• Food production (bread, beer, dairy)

• Biodegradation & bioremediation

• Commercial products

• Genetic engineering

• Normal flora protection

• Pathogens

• Model organisms

emerging diseases

Newly recognized or newly appearing diseases. Examples: SARS, MERS, Ebola, Hantavirus, Lyme disease, AIDS, Swine flu (H1N1), Hepatitis C.

re-emerging diseases

Previously controlled diseases that are increasing again. Examples: Measles, mumps, whooping cough, tuberculosis

why microorganisms are useful model organism

• Same metabolic pathways as higher organisms

• Same genetic principles

• Fast growth

• Easy to manipulate

• “What is true of elephants is also true of bacteria.”

Bacteria

• Prokaryotic

• Peptidoglycan cell wall

• 0.3–2 µm

• Unique rRNA sequences

• ester-linked lipids

• Ex: E. coli, Staphylococcus, Streptococcus

Archaea

• Prokaryotic

• No peptidoglycan

• Extremophiles

• Unique membrane lipids

• Unique rRNA sequences

• ether-linked lipids

• Extremophiles (thermophiles, halophiles)

Eukarya

• Eukaryotic

• Nucleus + organelles

• 5–50 µm

• Unicellular or multicellular

• Fungi (yeasts, molds, mushrooms use organic material)

• Algae (photosynthetic; use sunlight)

• Protozoa (single-celled, motile, ingest organic material)

• Helminths (worms, macroscopic adults but microscopic eggs/larvae)

Correct scientific naming

• Genus capitalized

• Species lowercase

• Italicized or underlined

• Example: Escherichia coli

• Abbreviation: E. coli

coccus

spherical

Rod/bacillus

cylindrical

vibrio

comma-shaped

spirillum

rigid spiral

spirochete

flexible spiral

Pleomophic

many shapes

diplococcus

pairs

streptococcus

chains

sarcina

cubical packets

staphylococcus

clusters

structure of Bacteria

peptidoglycan

ester-linked

everywhere

unique rRNA

hollow flagella

structure of archaea

no peptidoglycan

ether-linked

often in extreme environments

rRNA is unique but more similar to eukaryotes

solid flagella

have branched hydrocarbons

archaea protein synthesis resembles eukaryotes

virus structure

DNA or RNA + protein coat; obligate intracellular parasite

viroid

Only RNA; no protein coat; plant pathogens

prion

Only protein; misfolded; causes neurodegenerative disease; form fibrils, resist sterilization

size range of microorganisms

• Viruses: 20–300 nm

• Bacteria: 0.3–2 µm

• Eukaryotic cells: 5–50 µm

• Some bacteria visible to naked eye (Epulopiscium)

Light mircoscope

magnifies up to ~1,000×; used for most routine microbial observation

electron microscope

uses electrons instead of light; magnifies >100,000×; allows visualization of internal structures.

atomic force microscope

produces images of individual atoms on surfaces.

Prepping smear used in staining procedures

• Spread thin film of specimen on slide.

• Air dry.

• Heat-fix by passing through flame.

• Flood with stain, rinse, dry

• 
  

• Heat fixing kills bacteria and adheres them to slide.

• Thin smear prevents clumping.

Gram stain procedure + function

1. Crystal violet (primary stain) — stains all cells purple.

2. Iodine (mordant) — forms CV–iodine complex; cells remain purple.

3. Alcohol (decolorizer) —

   • Gram‑positive: remain purple (thick peptidoglycan retains dye).

   • Gram‑negative: become colorless (outer membrane disrupted).

4. Safranin (counterstain) —

   • Gram‑positive: stay purple.

   • Gram‑negative: appear pink.

• Alcohol is the critical step.

• Gram‑negative outer membrane increases vulnerability to alcohol.

prokaryotic structures within cells

• No membrane-bound nucleus

• No membrane-bound organelles

• DNA in nucleoid

• 70S ribosomes

• Cell wall usually present

• Divide by binary fission

• Typically 0.3–2 µm

• High surface-area-to-volume ratio → rapid growth

• Vulnerable to predators/parasites

prokaryotic cell wall

rigidity; prevents lysis

prokaryotic cytoplasmic membrane

selective barrier, energy generation

prokaryotic nucleoid

contains chromosome

prokaryotic plasmids

extra DNA; advantageous traits

prokaryotic Ribosomes (70S)

protein synthesis

prokaryotic flagella

motility

prokaryotic pili/fimbriae

attachment; conjugation

prokaryotic Capsule/slime layer

protection, adherence;

prokaryotic endospores

dormancy; extreme resistance; only in Bacillus & Clostridium

fluid mosaic model

The membrane is a phospholipid bilayer with proteins that float within it, allowing flexibility and dynamic movement.

• Membrane is semipermeable.

• Proteins act as gates and sensors.

Primary protein structure

amino acid sequence

secondary

a-helix or B-sheet (hydrogen bonds)

tertiary

3D folding

Quaternary

multiple polypeptides together