Microbiology Foundations: History, Germ Theory, Genomes & Cell Biology

What is a microbe?

A living organism that requires a microscope to be seen. Cells range from millimeters down to ~0.2 µm; viruses may be ten times smaller.

Which "contradictions" complicate the simple definition of a microbe?

Supersize cells (Thiomargarita namibiensis), microbial communities (biofilms), and viruses (e.g. mimivirus).

What are the three domains of life that microbes belong to?

Bacteria, Archaea, and Eukarya (microbes include members of all three).

What is a genome?

The total genetic information in an organism's chromosomal DNA.

Who developed the first DNA sequencing method fast enough for large genomes?

Fred Sanger (shared the 1980 Nobel Prize in chemistry).

First cellular microbe to have its genome sequenced (1995)?

The bacterium Haemophilus influenzae.

What is a metagenome?

The collection of sequences taken directly from the environment.

How have microbes shaped human history?

Food (bread, wine, cheese, chocolate), destroying crops (Irish Potato Famine), and disease (bubonic plague, smallpox in the Americas, COVID-19).

Who first recognized the importance of disease in warfare, and what did she invent?

Florence Nightingale; she founded medical statistics and devised the "polar area chart."

Who built the first compound microscope (mid-1600s)?

Robert Hooke; he observed small eukaryotes.

Who first observed single-celled organisms and discovered bacteria (1676)?

Antonie van Leeuwenhoek.

What is spontaneous generation?

The theory that living creatures could arise without parents.

What did Francesco Redi show (1660s)?

Maggots in decaying meat were offspring of flies, not spontaneously generated.

What did Lazzaro Spallanzani show (1760s)?

A sealed flask of meat broth sterilized by boiling failed to grow microbes.

What did Louis Pasteur's swan-neck flasks show (1860s)?

After boiling, the contents stayed free of microbial growth despite access to air. This disproved spontaneous generation. He also found the microbial basis of fermentation.

What is the germ theory of disease?

Many diseases are caused by microbes (transmission of germs causes disease). A scientific theory is NOT a "guess"; it explains observations, gives a framework, and can be tested.

Who founded the scientific method of microbiology and worked on anthrax?

Robert Koch, German physician.

Who introduced solid media with agar, and who invented the Petri dish?

Angelina and Walther Hesse introduced agar; Julius Petri made the double-dish container.

Why were pure cultures needed in Koch's work?

To prove a particular bacterium caused a specific disease.

Koch's Postulate 1?

The microbe is always present in the diseased host and absent in healthy hosts.

Koch's Postulate 2?

The microbe is grown in pure culture (no other microbes present).

Koch's Postulate 3?

Introduce the pure microbe into a healthy host and the individual becomes sick.

Koch's Postulate 4?

The same microbe is re-isolated from the now-sick individual.

Who introduced smallpox inoculation to Europe (1717)?

Lady Mary Montagu.

What did Edward Jenner do, and where does "vaccination" come from?

He deliberately infected patients with matter from cowpox lesions. Vaccination comes from Latin vacca = cow.

What did Pasteur's first vaccines use?

Attenuated (weakened) strains, for fowl cholera and rabies.

Define immunization.

Stimulation of an immune response by deliberate inoculation with an attenuated pathogen.

What did Ignaz Semmelweis do (1847)?

Ordered doctors to wash hands with chlorine (an antiseptic); mortality rates fell.

What did Joseph Lister do (1865)?

Developed carbolic acid to treat wounds and clean surgical instruments.

What is aseptic surgery?

Surgery done in environments completely free of microbes (developed in the 20th century).

Who discovered penicillin and when?

Alexander Fleming, 1929: Penicillium mold made a substance that kills bacteria.

Who purified penicillin (1941)?

Howard Florey and Ernst Chain; the first commercial antibiotic to save human lives.

How were viruses discovered?

Dmitri Ivanovsky (1892): tobacco mosaic disease agent passed through a porcelain filter that blocked all known microbes. Beijerinck concluded it was not a bacterium. Wendell Stanley purified and crystallized it (tobacco mosaic virus, TMV).

What roles do microbes play in ecology, and how much can we culture?

They cycle minerals essential for life, including all global N2 and much of O2. Less than 0.1% of microbial species can be cultured in the lab.

Who was Sergei Winogradsky?

Russian scientist, an early student of microbes in natural habitats. Discovered lithotrophs, developed enrichment cultures, and built the Winogradsky column (a wetland model ecosystem). Showed bacteria's importance in geochemical cycling.

What are endosymbionts? Give an example.

Microbes living symbiotically inside a larger organism. Rhizobia induce legume roots to form nodules for nitrogen fixation.

State the endosymbiont theory (Lynn Margulis).

Mitochondria were once bacteria and chloroplasts were once cyanobacteria, engulfed by or infecting other cells and ending up living together inside them.

Evidence that organelles came from bacteria?

Mitochondrial and chloroplast DNA is similar to bacterial DNA.

Why was endosymbiosis controversial?

It implied a polyphyletic ancestry (not only divergence from a common ancestor, which is monophyletic).

How are archaea different from bacteria?

Similar size and shape but very different biochemistry: different membranes, and archaeal ribosomes resemble eukaryotic ribosomes. Many live in harsh environments. They are a separate domain.

Who discovered archaea and how?

Carl Woese (1977) by analyzing 16S rRNA of prokaryotes from hot springs and methane producers. 16S rRNA gene sequence is found in all creatures.

Name three cell biology techniques and what each does.

Electron microscopy (cell components, organelles, membranes), ultracentrifuge (separate components), fluorescence microscopy (subcellular location of proteins).

Who discovered the DNA double helix structure?

Rosalind Franklin (discovered the double helix); also credited: James Watson, Francis Crick, Maurice Wilkins.

Which organism has the best understood genome?

E. coli.

What format is the midterm?

Multiple choice and true/false on Gradescope scantrons, approximately 30 questions.

Final exam date and time?

December 9th, 2026, 8:00-11:00 AM. No make-up midterms without a doctor's note.

Main structural differences between prokaryotes and eukaryotes?

Prokaryotes have no defined organelles and their DNA is not bounded by a membrane. They are generally much smaller (about the size of a eukaryotic mitochondrion).

Why does small size help prokaryotes?

Large surface area/volume ratio means more rapid transport: faster waste excretion and nutrient import.

Bacterial cell shapes?

Cocci = spheres; bacilli = rods/sticks; vibrios = bent rods; spiral; irregular. Cocci and bacilli can be alone, in chains, or in bunches.

Monomorphic vs pleomorphic?

Monomorphic = one shape (most pure cultures). Pleomorphic = multiple shapes; changes during growth (cells get smaller with age) or in response to cues like sporulation (nutrient limitation).

What is the nucleoid?

A system of looped coils of DNA in the cytoplasm; no membrane separates it from the cytoplasm.

Facts about the bacterial chromosome?

Single loop of double-stranded DNA, one molecule, ~4x10^6 bp in most bacteria, compacted by supercoiling, attached to the cell envelope, replicates once per cell division.

How is the nucleoid organized?

About 50 looped domains; within each, DNA is supercoiled and partly compacted by DNA-binding proteins.

What makes up the cell envelope?

Cell membrane + cell wall + outer membrane (if there is one). It differs between Gram+ and Gram- bacteria.

Structure of the cell membrane?

Lipid bilayer of phospholipids (fatty acids = hydrophobic, glycerol-phosphate = hydrophilic). Permeability barrier with embedded proteins that anchor membranes to the envelope, sense the outside, and transport materials.

Passive vs active transport (Lecture 3-4)?

Passive follows the gradient of the material. Active transport uses pumps with energy (ATP or PMF) to move material against its gradient.

How do proton pumps generate PMF?

They push protons out of the cell. Osmotic and electrical forces push protons back in. ATP synthase uses PMF to make ATP.

What does the bacterial cell wall do?

Rigid structure just outside the cytoplasmic membrane; lets bacteria withstand turgor pressure from dissolved solutes. Two major types: Gram positive (thick) and Gram negative (thin).

What is peptidoglycan and why does it matter?

The polymer of the bacterial cell wall (murein). Its synthesis is unique to bacteria, so it is a common antibiotic target (penicillin).

What is the sacculus?

The bacterial cell wall: a single interlinked molecule of peptidoglycan that gives shape and rigidity.

Structure of peptidoglycan?

Sugar (glycan) chains wrapped around the cell, linked to each other by short peptide (amino acid) crosslinks.

What sugars make up the glycan part?

NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid) disaccharide units; four amino acids are linked by peptide bonds.

Gram+ vs Gram- peptidoglycan crosslinks?

Gram-: direct cross-linking, thin layer. Gram+: peptide interbridge, thick layer.

List the Gram-positive envelope layers.

Capsule (not all species, polysaccharide), S layer (not all, protein), thick cell wall (9-amino acid crosslinks, teichoic acids for strength), thin periplasm, plasma membrane.

List the Gram-negative envelope layers.

Capsule (not all species), outer membrane (lipopolysaccharide in outer leaflet only), thin cell wall (4-amino acid crosslinks), thick periplasm, plasma (inner) membrane.

Gram+ vs Gram- thickness summary?

Gram+: thick wall, thin periplasm, no outer membrane. Gram-: thin wall, thick periplasm, outer membrane with LPS.

What is the Gram stain?

Developed by Hans Christian Gram in 1884. The most widely used stain; a differential stain based on cell wall composition. Gram positive = blue (purple), Gram negative = pink.

Glycocalyx vs capsule vs S-layer?

Glycocalyx: network of polysaccharides from the cell surface (survival, attachment, virulence). Capsule: a well organized glycocalyx, difficult to remove. S-layers: protein or glycoprotein layers, common among Archaea.

Gene expression in bacteria?

RNA polymerase transcribes DNA to mRNA; the ribosome translates RNA to protein. The processes occur simultaneously.

How does a bacterial cell divide?

Cell elongates (adds new wall at the equator), DNA replicates bidirectionally (can begin the next round before division), then septation, usually at the equator.

Bacterial cytoskeleton proteins?

FtsZ forms the Z-ring (spherical cells; division), MreB forms a coil in rod-shaped cells, CreS (crescentin) forms a polymer along the inner side of crescent-shaped bacteria. They determine shape.

Fimbriae and pili functions?

Thin protein filaments (pilin) that attach cells to surfaces. Sex pili are used in conjugation; essential for pathogenicity; receptors for viruses. Stalks are cytoplasm extensions that attach cells.

Three parts of a flagellum?

Filament (flagellin), hook (hook protein), and basal body (rings).

Monotrichous vs lophotrichous vs peritrichous?

Monotrichous (polar): a single flagellum at one end. Lophotrichous: a tuft at one or both ends. Peritrichous: flagella on all sides.

How do reversible polar flagella move?

CCW rotation = forward swimming; CW rotation = reversal of direction.

How do peritrichous flagella move?

CCW rotation forms a bundle = smooth swimming (a run). CW rotation disaggregates the bundle = tumble, which reorients the cell.

What is chemotaxis?

Movement toward or away from specific chemicals. Runs and tumbles make a random walk; attractants (sugars, amino acids) suppress tumbles so runs get longer, giving a biased random walk toward the attractant.

Attractants vs repellents?

Attractants (nutrients): cells move up the gradient, tumbles are suppressed, runs lengthen. Repellents (wastes, toxic chemicals): cells move down the gradient.

Essential nutrients?

Those that must be supplied from the environment.

Macronutrients vs micronutrients?

Macronutrients: major elements in macromolecules (C, O, H, N, P, S) plus cations needed for protein function. Micronutrients: trace elements needed for enzyme function.

Autotroph vs heterotroph?

Autotrophs fix CO2 into organic molecules (mainly sugars). Heterotrophs use preformed organic molecules.

Phototroph vs chemotroph?

Phototrophs get energy from light-triggered reactions. Chemotrophs get energy from oxidation-reduction reactions.

Lithotroph vs organotroph?

Lithotrophs use inorganic molecules as electron source. Organotrophs use organic molecules.

Classify microbes by carbon and energy source.

Autotrophs: photoautotrophs, chemolithoautotrophs (lithotrophs). Heterotrophs: photoheterotrophs, chemoheterotrophs (organotrophs).

What is proton motive force (Lecture 5-6 definition)?

The H+ gradient plus the charge difference across the membrane (an electrochemical potential), created when chemical energy pumps protons out. It powers nutrient transport, flagellar rotation, and ATP synthesis by F1Fo ATP synthase.

Passive diffusion?

Some gases (O2, CO2) pass freely through membranes, following their gradient.

Facilitated diffusion?

Transporters move material along its gradient with no cellular energy. Cannot move a molecule against its gradient. Example: glycerol transporter.

Symport vs antiport?

Both use the gradient of one molecule (e.g. H+) to move another against its gradient. Symport: both move in the same direction. Antiport: the transported molecule moves opposite to the driving ion.

ABC transporters?

ATP-binding cassette superfamily. Use ATP energy to move material into the cell against its gradient.

Phosphotransferase system (PTS)?

Uses energy from phosphoenolpyruvate (PEP) to bring material in and modifies it as it enters. Example: glucose becomes glucose-6-phosphate, which cannot leave, so the gradient is maintained and more glucose flows in.

Name the active transport systems.

Simple active transport (symport and antiport), ABC transporters, and PTS.

What fraction of microbes have been cultured?

Less than 1% after 120 years of trying (the lecture also cites under 0.1% of species).

Liquid vs solid culture media?

Liquid (broth): study growth characteristics of a pure culture. Solid (usually agar): separate mixed cultures from clinical or environmental samples.

Two ways to isolate pure colonies?

Dilution streaking (drag a loop across an agar plate) and spread plate (tenfold serial dilutions of a liquid culture, plate a small amount of each).

How do you calculate CFU/ml from a spread plate?

Colonies counted divided by (dilution factor x volume plated). The slide example: 27 colonies at the 10^-5 dilution, x10 to convert to per ml, gives 2.7 x 10^7 CFU/ml.

Complex media?

Enriched, unknown exact composition (e.g. nutrient agar, LB). Contains vitamins, amino acids, growth factors. Auxotrophs and prototrophs both grow.

Defined media?

Synthetic; all constituents known (e.g. M9). Only components needed to grow; only prototrophs grow unless supplemented.

Selective media?

Favors growth of particular microbes while inhibiting others. Minimal media select for prototrophs. No universal medium grows all microbes.

Differential media?

Used to distinguish and identify microbes based on biological characteristics.

Why is MacConkey agar both selective and differential?

Selective: only Gram-negative bacteria grow. Differential: lactose fermenters turn red (distinguishes E. coli from Salmonella).