Difficulty: Introductory to Intermediate | Prerequisites: Weeks 3–4 chemistry (osmotic principles, solubility). Familiarity with basic cell biology helpful but not essential.
This set of notes covers a wide arc of the CM101 microbiology content: from the basic distinction between prokaryotic and eukaryotic cells (Week 5), through bacterial classification and growth requirements (Weeks 5–6), to viruses (Week 6), and then the Week 7 lecture material on protozoans and fungi. These are the organisms (and non-living agents) that matter in mortuary science, because they are the things that cause infection, drive decomposition, and determine how an embalmer approaches a case. If you have missed recent lectures, start here.
All life is built from either prokaryotic cells (no nucleus, simpler) or eukaryotic cells (nucleus, organelles). Bacteria are prokaryotes classified by shape, arrangement, and growth needs. Viruses are non-living obligate intracellular parasites made of genetic material plus a protein coat. Protozoans are single-celled eukaryotic parasites classified into four groups (amoeba, flagellates, ciliates, apicomplexans) and cause roughly 20% of infectious diseases worldwide. Fungi are heterotrophic eukaryotes split into macroscopic (mushrooms) and microscopic (yeasts and moulds) forms, and cause infections ranging from superficial skin conditions to life-threatening respiratory disease.
Prokaryote
A cell that lacks a true membrane-bound nucleus. Its DNA is found in a region called the nucleoid. Bacteria are prokaryotes. Think of it as the simpler, older model of cell.
Eukaryote
A cell with a true membrane-bound nucleus and organelles (mitochondria, ER, Golgi, etc.). Protozoans, fungi, plants, and animals are eukaryotes.
Capsule (bacterial)
A protective layer of polysaccharides surrounding some bacterial cells. It shields bacteria from phagocytosis by the host immune system and helps them stick to surfaces. Stains negatively. In simple terms, it is a sticky armour coat.
Cocci
Spherical bacteria. Arrangements include monococcus (single), diplococcus (pairs), streptococcus (chains), tetracoccus (tetrads), staphylococcus (grape-like clusters), and sarcina (3D cubes).
Bacilli
Rod-shaped bacteria.
Spirals
Spiral-shaped bacteria, subdivided into vibrio (curved rod), spirillum (inflexible corkscrew), and spirochete (flexible corkscrew).
Psychrophile
A bacterium that thrives in cold temperatures.
Mesophile
A bacterium that prefers moderate temperatures. Most human pathogens are mesophiles.
Thermophile
A bacterium that thrives in high temperatures, such as hot springs.
Autotroph
An organism that makes its own food from inorganic substances (via photosynthesis or chemosynthesis).
Heterotroph
An organism that must obtain nutrition from pre-formed organic compounds. All fungi and many bacteria are heterotrophs.
Obligate intracellular parasite
An organism (or agent) that can only reproduce inside a host cell. All viruses are obligate intracellular parasites.
Capsid
The protein coat surrounding a virus's genetic material. Think of it as the shell around the virus's DNA or RNA.
Protozoan
A single-celled, free-living eukaryote. Parasitic forms cause diseases such as malaria and giardiasis.
Dermatophyte
A fungus with a predilection for keratin, the protein in skin, hair, and nails. Dermatophytes cause tinea (ringworm) infections.
Hyphae
The thread-like filamentous structures formed by moulds. A mass of hyphae is called a mycelium.
Mycosis
Any fungal infection. Classified by portal of entry: primary/respiratory, cutaneous, or subcutaneous.
Spore (fungal)
A reproductive structure produced by fungi. Can be asexual or sexual and is often used to identify fungal species.
All life is built from one of two cell types:
Prokaryotic cells: no true nucleus, DNA in a nucleoid region. Structures include cell wall, plasma membrane, cytoplasm, ribosomes, and sometimes a capsule, pili, and flagellum.
Eukaryotic cells: membrane-bound nucleus plus organelles (mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, centrioles, peroxisomes, cytoskeletal elements).
The capsule is a polysaccharide layer secreted by some bacteria. It serves two main functions: protecting the bacterium from phagocytosis by the host immune system, and aiding adhesion to surfaces. Capsule-producing bacteria often stain negatively, and many pneumonia-causing bacteria have capsules.
Bacteria come in three basic shapes:
Cocci (spherical)
Bacilli (rod-shaped)
Spirals, which subdivide into:
Vibrio: curved rod
Spirillum: inflexible corkscrew
Spirochete: flexible corkscrew
Cocci are further classified by how they group after division:
Monococcus: occurring singly
Diplococcus: in pairs
Streptococcus: in chains
Tetracoccus: in tetrads (groups of four)
Staphylococcus: in grape-like clusters
Sarcina: in 3D geometrical (cube-like) forms
Psychrophiles: thrive in cold temperatures.
Mesophiles: prefer moderate temperatures. Most human pathogens fall here.
Thermophiles: thrive in high temperatures (hot springs, geothermal areas).
Bacteria are classified by how they obtain energy:
Autotrophic bacteria make their own organic compounds from inorganic substances, using photosynthesis or chemosynthesis (e.g. reactions involving sulfur or ammonia).
Heterotrophic bacteria rely on pre-formed organic compounds. They subdivide by their relationship with a host:
Strict (obligate) saprophytes: feed exclusively on dead organic matter. They drive decomposition and nutrient recycling.
Strict (obligate) parasites: rely on a living host for nutrition and often cause disease.
Facultative saprophytes: can switch between dead organic matter and living hosts.
Facultative parasites: typically saprophytic but can become parasitic under certain conditions.
Other growth requirements covered in this course include energy, oxygen, water, pH, radiation, and osmotic pressure.
Viruses are sub-cellular infectious agents, typically 10–100 times smaller than bacteria.
Most viruses consist of two parts:
Genetic material: either DNA or RNA (never both).
Capsid: a protein coat surrounding the genetic material.
Some viruses, including many that infect humans, also have a lipid envelope surrounding the capsid.
Viruses lack true cellular structures found in prokaryotes and eukaryotes. They are therefore generally considered non-living infectious particles. Because they cannot reproduce outside a host cell, they must be grown in tissue culture (often inside eggs) in the laboratory. All viruses are obligate intracellular parasites.
A series of steps allows viruses to infect cells:
Attachment: the virus binds to the host cell surface.
Penetration: the virus (or its genetic material) enters the host cell.
Replication/Biosynthesis: the host cell's machinery is hijacked to copy viral genetic material and produce viral proteins.
Maturation/Assembly: new viral particles are assembled from the components.
Release (Lysis): new viruses break out of the host cell, often destroying it, and go on to infect other cells.
Protozoans are single-celled, free-living eukaryotes. Protozoan parasites are classified into four groups based on their mode of movement.
Amoeba (Ameba): move by extending pseudopods ("false feet") along surfaces. Typically associated with digestive system infections. Entamoeba histolytica is the key example. In rare cases they can infect the liver or brain. They cannot live freely in liquid environments because they require a surface to "walk" along.
Flagellates: move using whip-like flagella. Also often associated with the digestive system. They can survive free-living in liquid environments for extended periods. Giardia intestinalis lives in water and is transmitted through drinking contaminated water.
Ciliates: move using cilia (fine hairs covering the cell surface). Balantidium is a genus of ciliates that infects the digestive system.
Apicomplexans: a group that includes Plasmodium falciparum, one of the parasites that causes malaria. Plasmodium infects red blood cells.
Protozoans are transmitted via:
Human contact (including through contaminated food and water)
Arthropod vectors (insects, e.g. mosquitoes transmitting malaria)
Protozoans account for roughly 20% of all infectious diseases annually. Most protozoan infections are acquired in developing nations. Malaria alone causes over 200 million cases and more than 400,000 deaths worldwide per year.
Protozoan infections are managed through:
Antiprotozoal drugs (e.g. quinine and artesunate for malaria, metronidazole for amebiasis and giardiasis)
Proper hygiene (especially food and water sanitation)
Vector control (reducing insect populations that transmit the parasites)
Fungi fall into two main groups:
Macroscopic fungi: mushrooms. While mushrooms can produce chemicals that make humans ill, they are not infectious.
Microscopic fungi: yeasts and moulds. Moulds form thread-like structures called hyphae; a mass of hyphae is a mycelium.
Fungi are heterotrophs, meaning they cannot photosynthesise and must obtain nutrition from external sources. They can draw energy from a wide range of substrates, which is why they grow on surfaces other organisms cannot: hair, rubber, skin, and wood.
Fungi tolerate a wide range of salt, sugar, acid, and high-temperature environments.
Fungi reproduce via spores, which can be either asexual or sexual. Spore type is often used as a means to identify fungal species.
Most pathogenic fungi are found in soil or air. Fungal diseases are typically not communicable (not passed person to person).
Dermatophytes are fungi with specialised enzymes that break down keratin, the tough protein in skin, hair, and nails. They cause superficial infections collectively called "tinea" or ringworm.
Key tinea infections:
Tinea corporis (ringworm): red, circular, itchy rashes on the body. Transmitted via contact with infected individuals, pets, or contaminated objects.
Tinea capitis (scalp ringworm): affects the scalp and hair. Can cause hair loss. Often affects children. Transmitted through shared combs, brushes, or hats.
Tinea cruris (jock itch): red, itchy rashes in the groin area and inner thighs. More common in males.
Tinea pedis (athlete's foot): itching, peeling, and blisters on the feet, particularly between the toes. One of the most common fungal infections. Picked up in public showers and locker rooms.
Tinea unguium (onychomycosis): affects the nails, causing discoloration, thickening, and brittleness. Difficult to treat, often requiring long-term therapy.
Dermatophyte infections are generally superficial, affecting only the outermost layers of skin, hair, and nails. They do not typically invade deeper tissues or organs.
Transmission occurs through direct contact with infected individuals, animals, or contaminated surfaces. Warm, moist environments facilitate growth.
Treatment involves topical and oral antifungal medications, chosen based on location and severity. Prevention measures include keeping skin dry and avoiding shared personal items.
Primary (respiratory) mycoses: inhaled. Example: Histoplasma, which can cause severe and even fatal respiratory infections, especially in immunocompromised individuals.
Cutaneous (superficial) mycoses: on the skin. The tinea infections described above.
Subcutaneous mycoses: enter through injured skin. Often caused by the same agents as cutaneous infections, but because they penetrate below the epidermis they tend to cause chronic infections requiring aggressive treatment, including debridement (removal of dead or injured tissue).
Primary (true) pathogens: can infect otherwise healthy individuals. Tend to be geographically restricted. Example: Histoplasma capsulatum, endemic to the Ohio River Valley and Mississippi River states in the US. It is a soil fungus that causes lung infections when inhaled.
Opportunistic pathogens: tend to infect individuals with compromised immune systems. Found worldwide. Example: Candida albicans, part of the normal flora that causes infection when the immune system is weakened.
Students often think viruses are living organisms. They are not. Viruses lack cellular structures, cannot reproduce independently, and are classified as non-living infectious particles.
Students frequently confuse the four protozoan groups. The key distinguishing feature is mode of movement: pseudopods (amoeba), flagella (flagellates), cilia (ciliates), or none/specialised apical complex (apicomplexans).
Students sometimes assume all fungal infections are contagious. Most fungal diseases are not communicable. Dermatophyte infections (tinea) are an exception, as they can spread through direct contact or shared items.
Ringworm is not caused by a worm. The name refers to the circular shape of the rash. It is a fungal infection caused by dermatophytes.
⚠️ Be able to distinguish prokaryotic from eukaryotic cells and list their key structural differences.
⚠️ Know the three bacterial shapes (cocci, bacilli, spirals) and the six cocci arrangements by name.
⚠️ Know the five steps of viral replication in order: attachment, penetration, biosynthesis, maturation/assembly, release (lysis).
⚠️ Be able to name the four protozoan groups and give one example organism for each.
⚠️ Know the five tinea infections by their Latin names and body location (corporis = body, capitis = scalp, cruris = groin, pedis = feet, unguium = nails).
⚠️ Understand the difference between primary (true) fungal pathogens and opportunistic fungal pathogens, with one example of each.
⚠️ The distinction between autotroph and heterotroph, and the four subtypes of heterotrophic bacteria, is likely exam material.
True or false: Bacteria are eukaryotes. (False. Bacteria are prokaryotes.)
Fill in the blank: A grape-like cluster of cocci is called ________. (Staphylococcus.)
True or false: Viruses can reproduce on their own outside a host cell. (False. They are obligate intracellular parasites.)
Fill in the blank: The protozoan that causes malaria by infecting red blood cells is Plasmodium ________. (falciparum.)
True or false: Fungal diseases are typically communicable. (False. Most are not communicable.)
Q: Name the four groups of protozoan parasites and state how each moves.
A: Amoeba (pseudopods), flagellates (flagella), ciliates (cilia), and apicomplexans (specialised apical complex, no conventional motility structure).
Q: A patient presents with a fungal skin infection on their inner thigh. What is the Latin name for this condition, and what type of organism causes it?
A: Tinea cruris (jock itch), caused by dermatophytes.
Q: Explain why viruses are considered non-living.
A: Viruses lack true cellular structures (no ribosomes, no membrane-bound organelles, no metabolic machinery). They cannot reproduce independently and must hijack a host cell's machinery to replicate. They are therefore classified as non-living infectious particles.
Q: What is the difference between a primary (true) fungal pathogen and an opportunistic fungal pathogen? Give one example of each.
A: A primary pathogen can infect otherwise healthy individuals and tends to be geographically restricted (e.g. Histoplasma capsulatum in the Ohio/Mississippi River valleys). An opportunistic pathogen tends to infect immunocompromised individuals and is found worldwide (e.g. Candida albicans).
Q: List the five steps of the viral replication cycle in order.
A: Attachment, penetration, replication/biosynthesis, maturation/assembly, release (lysis).
Q: What structures does a prokaryotic cell have that a eukaryotic cell does not, and vice versa?
A: Prokaryotes have a nucleoid (no membrane-bound nucleus), and may have a cell wall, capsule, and pili. Eukaryotes have a true nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, and other membrane-bound organelles that prokaryotes lack.
The prokaryote/eukaryote distinction matters for understanding why antibiotics work on bacteria but not on human cells (different ribosome types, different cell wall chemistry).
Protozoan transmission through vectors connects to public health and epidemiology topics later in the course.
Fungal keratin-digesting enzymes tie back to the organic chemistry of proteins and enzyme function, which appears in later units.
The viral replication cycle is the foundation for understanding antiviral drug targets and how vaccines work, both covered later.
Prokaryote, eukaryote, cell organisation, cell wall, plasma membrane, nucleoid, capsule, pili, flagellum, cocci, bacilli, spirals, vibrio, spirillum, spirochete, monococcus, diplococcus, streptococcus, staphylococcus, tetracoccus, sarcina, psychrophile, mesophile, thermophile, autotroph, heterotroph, saprophyte, parasite, facultative, obligate, virus, viroid, capsid, lipid envelope, obligate intracellular parasite, viral replication, lytic cycle, attachment, penetration, biosynthesis, maturation, lysis, protozoan, amoeba, flagellate, ciliate, apicomplexan, Entamoeba histolytica, Giardia intestinalis, Balantidium, Plasmodium falciparum, malaria, vector, arthropod, fungus, fungi, yeast, mould, mold, hyphae, mycelium, spore, heterotroph, dermatophyte, keratin, tinea, ringworm, tinea corporis, tinea capitis, tinea cruris, tinea pedis, tinea unguium, onychomycosis, athlete's foot, jock itch, mycosis, primary mycosis, cutaneous mycosis, subcutaneous mycosis, Histoplasma, Histoplasma capsulatum, Candida albicans, opportunistic infection, CM101, mortuary science microbiology