Chapter 1 · Chapter 3 · Chapter 4

Reference sheets

Everything on one long page, laid out to print. Nine sheets, no interaction, nothing that needs a screen.

Sheet 1 — Cell structures

Structure	Where	In	Made of	Does
Capsule	Outside the wall	Some	Polysaccharides, polypeptides, or both, in organised repeating units	A firmly attached glycocalyx. Protects the cell and helps it evade the host.
Slime layer	Outside the wall	Some	Polysaccharides, water soluble	A loosely attached, sticky glycocalyx that lets the cell attach to surfaces.
Flagellum	Outside the wall	Some	Filament, hook and basal body; the basal body anchors through rings of integral protein	Movement. Rotation propels the cell, and it can turn either way.
Fimbriae	Outside the wall	Some	Protein	Sticky, bristle-like projections used to stick to surfaces, to hosts, and to each other.
Pilus (conjugation pilus)	Outside the wall	Some	Protein	Transfers DNA from one cell to another — conjugation.
Cell wall	Cell wall	Most	Peptidoglycan — alternating NAG and NAM sugars, cross-linked by peptide bridges	Gives the cell its shape, holds it together against osmotic pressure, and helps some cells attach.
Cytoplasmic membrane	Membrane	All	Phospholipid bilayer with embedded proteins	Controls what enters and leaves. Also where energy production happens, since bacteria have no mitochondria.
Cytoplasm	Inside the cell	All	Mostly water, with dissolved ions, sugars, amino acids and enzymes	The medium every reaction in the cell takes place in.
Nucleoid	Inside the cell	All	A single circular chromosome of DNA	Holds the genome.
Plasmid	Inside the cell	Some	Small circular DNA, separate from the chromosome	Carries extra genes the cell does not strictly need to survive.
Ribosome	Inside the cell	All	70S in bacteria — a 50S and a 30S subunit	Builds proteins.
Inclusions	Inside the cell	Some	Stored nutrients — lipid, glycogen, phosphate, sulfur	A reserve the cell draws on when supplies run short.
Endospore	Inside the cell	Some	A dehydrated core wrapped in tough protein coats, with dipicolinic acid and calcium	A dormant survival structure, not a reproductive one — one cell makes one spore.

Sheet 2 — Prokaryote vs eukaryote

Feature	Prokaryotic	Eukaryotic
Nucleus	None — DNA sits in the cytoplasm in a region called the nucleoid	A true nucleus, bounded by a membrane
Chromosome	One circular chromosome, often with plasmids	Several linear chromosomes, wound on histones
Membrane-bound organelles	None	Mitochondria, ER, Golgi, lysosomes and more
Ribosomes	70S — a 50S and a 30S subunit	80S — a 60S and a 40S subunit
Cell wall	Peptidoglycan in bacteria; other polymers in archaea	Cellulose in plants, chitin in fungi, none in animals
Size	About 1 µm	10 to 100 µm
Division	Binary fission	Mitosis or meiosis
Cytoskeleton	Simple	Complex — microtubules, actin, intermediate filaments
Flagellum	Filament, hook, basal body; rotates	A 9+2 arrangement of microtubules; whips
Examples	Bacteria, archaea	Fungi, protozoa, algae, plants, animals

Sheet 3 — The Gram stain

Fig. AThe four steps and what each cell type looks like after each one.

Step	Reagent	Role	Gram +	Gram −
1	Crystal violet	Primary stain	Purple	Purple
2	Gram's iodine	Mordant	Purple	Purple
3	Alcohol or acetone	Decolouriser	Purple	Colourless
4	Safranin	Counterstain	Stays purple	Pink

Type	Peptidoglycan	Membranes	Colour
Gram-positive	Thick layer	One membrane, beneath the peptidoglycan	Purple
Gram-negative	Thin layer	Two membranes — one below and one above the peptidoglycan	Pink

Mistake	Result	Because
Over-decolourising	Gram-positive cells read as negative	Leave the alcohol on too long and even thick peptidoglycan gives up the crystal violet. This is the most common error by far.
Under-decolourising	Gram-negative cells read as positive	Too little alcohol and the complex never washes out of the thin wall.
Smear too thick	Patchy or falsely positive	Alcohol cannot reach the cells in the middle of a heavy smear.
Culture too old	Gram-positive cells read as negative	Ageing cells lose wall integrity, so old cultures stain unreliably. Use a culture 18–24 hours old.
Skipping the iodine	Everything reads as negative	Without the mordant the crystal violet is small enough to wash straight out of either wall.

Sheet 4 — Staining methods

Stain	Kind	Reagents	Shows	Reads as
Simple stain	simple	One basic dye — methylene blue, crystal violet or safranin	Shape, size and arrangement	Every cell the same colour
Negative stain	negative	An acidic dye such as nigrosin or India ink	Capsules, and cell shape without heat distortion	Dark background, clear cells
Gram stain	differential	Crystal violet, iodine, alcohol, safranin	Cell wall type	Purple is positive, pink is negative
Acid-fast stain	differential	Carbolfuchsin, acid-alcohol, methylene blue	Waxy mycolic acid in the wall	Red is acid-fast, blue is not
Endospore stain	structural	Malachite green with heat, then safranin	Endospores inside or outside the cell	Green spore, pink cell
Capsule stain	structural	Negative stain plus a simple counterstain	The capsule	Clear halo around a stained cell on a dark field
Flagella stain	structural	A mordant that builds up on the flagellum, then a stain	Number and placement of flagella	Flagella thick enough to see by light microscope

Sheet 5 — Shape and arrangement

Fig. BThe six shapes.

Fig. CThe six arrangements.

Sheet 6 — Microscopy

Objectives

Lens	Power	NA	With 10× ocular
Scanning	4×	0.10	40×
Low power	10×	0.25	100×
High dry	40×	0.65	400×
Oil immersion	100×	1.25	1000×

Care and use

1Carry it with one hand on the arm and the other under the base, always.
2Start on the lowest power objective and work up.
3Use the coarse adjustment only on low power; on 40× and 100× use fine adjustment alone.
4Immersion oil goes on the 100× objective only. Oil on a 40× lens ruins it.
5Clean lenses with lens paper only — anything else scratches the glass.
6Return to the lowest power, lower the stage, and remove the slide before putting it away.

Sheet 7 — Every formula

For	Formula	Watch for
Total magnification	ocular × objective	Multiply, never add. 10 × 100 = 1000×.
Resolving power	d = 0.61 λ ÷ NA	Smaller d is better. A light microscope stops at about 200 nm.
Useful magnification	≈ 1000 × NA	Past this you get empty magnification.
Field of view	field number ÷ objective power	The field shrinks as you go up in power.
Serial dilution	sample ÷ (sample + diluent), per tube	Dilutions multiply down the series.
Plate count	CFU/mL = colonies ÷ (volume plated × dilution)	Only count a plate between 25 and 250.
Binary fission	N = N₀ × 2ⁿ	n is the number of generations: time ÷ generation time.

Growth phases

Phase	Number	Why
Lag	No increase in number	Cells are making enzymes and building blocks, getting ready to divide. Metabolically busy, numerically flat.
Log (exponential)	Doubling at a constant rate	Conditions are ideal and nothing is limiting. This is where generation time is measured, and where cells are most sensitive to antibiotics.
Stationary	Number holds steady	Division and death balance out as nutrients run low and waste builds up.
Death (decline)	Numbers fall	Death outpaces division. Some cells form endospores here rather than die.

Sheet 8 — Media, history and taxonomy

Media

Medium	Kind	Reads
Nutrient agar	General purpose	Grows most non-fastidious bacteria. A general purpose plate.
Tryptic soy agar	General purpose	A richer general purpose medium.
MacConkey agar	Selective	Selective for Gram-negatives; also differential — pink colonies ferment lactose, colourless ones do not.
Mannitol salt agar	Selective	Selective for staphylococci; differential too — yellow means mannitol was fermented, which points to S. aureus.
Eosin methylene blue	Selective	Selective for Gram-negatives; E. coli gives a green metallic sheen.
Blood agar	Enriched	Enriched and differential — beta is complete clearing, alpha is green partial, gamma is none.
Chocolate agar	Enriched	Grows fastidious organisms such as Haemophilus and Neisseria.
Thioglycollate broth	Transport / special	Where growth sits in the tube shows the oxygen requirement.

Koch’s postulates

1The microorganism must be observed in every case of the disease.
2It must be isolated and grown in pure culture.
3The pure culture, when inoculated into an animal, must reproduce the disease.
4The microorganism must be recovered from the diseased animal.

Who did what

Who	Credited with
Robert Hooke	Named the cell
Antonie van Leeuwenhoek	First saw living microbes
Francesco Redi	First challenge to spontaneous generation
John Needham	Argued for spontaneous generation
Lazzaro Spallanzani	Argued against it
Louis Pasteur	Settled the question
Robert Koch	Linked one microbe to one disease
Joseph Lister	Antiseptic surgery
Ignaz Semmelweis	Handwashing
Florence Nightingale	Sanitation and nursing
John Snow	Epidemiology
Edward Jenner	Vaccination
Paul Ehrlich	Chemotherapy

Domains and ranks

Domain	Cell	Wall
Bacteria	Prokaryotic	Peptidoglycan
Archaea	Prokaryotic	No peptidoglycan
Eukarya	Eukaryotic	Cellulose, chitin or none

Domain · Kingdom · Phylum · Class · Order · Family · Genus · Species

Two parts: the genus first, then the species epithet.
The genus is capitalised; the species epithet is not.
Both parts are italicised, or underlined when written by hand.
After the first use the genus may be abbreviated to its initial — E. coli.
The species epithet is never used on its own.

Sheet 9 — Glossary

Aseptic technique: Working so that nothing unwanted gets into the culture, and nothing from the culture gets out.
Biofilm: A community of cells stuck to a surface in a matrix they secrete. Far harder to kill than free cells.
CFU: Colony-forming unit. One colony came from one unit, which may have been a clump of cells rather than one cell.
Chemotaxis: Movement toward or away from a chemical. Runs and tumbles, biased by what the cell senses.
Conjugation: DNA transfer between two cells through a pilus.
Endotoxin: Lipid A, part of the LPS in a Gram-negative outer membrane. Released when the cell dies.
Etiology: The cause of a disease. Koch’s postulates establish an etiologic relationship.
Fastidious: Needing unusual nutrients to grow. Why enriched media exist.
Fomite: An inanimate object that carries infection — a doorknob, a stethoscope, a phone.
Glycocalyx: The sugar coat outside the wall. Capsule if firm and organised, slime layer if loose.
Mordant: A reagent that fixes a stain in place. Iodine in the Gram stain.
Numerical aperture: How much light a lens gathers. It sets resolution, and oil raises it.
Peptidoglycan: The bacterial wall polymer: NAG and NAM sugars cross-linked by peptides.
Pure culture: A population grown from a single cell, so every organism in it is the same.
Taxis: Directed movement in response to a stimulus.
Teichoic acid: Poly-alcohols running through a Gram-positive wall. Gram-negatives have none.
Virulence factor: Anything that helps an organism cause disease — a capsule, a toxin, fimbriae.