Microbiology: Microorganisms, Cell Types, and Laboratory Techniques

What does microbiology study?

Microbiology studies microorganisms and acellular infectious agents, including their structure, function, ecology, disease roles, and practical uses.

Which groups are studied in microbiology?

Bacteria, archaea, protozoa, fungi, helminths, algae, viruses, and prions.

Which item is not considered a microbe in this course: bacterium, alga, mushroom, or protozoan?

Mushroom. It is a macroscopic fungus, whereas microbiology focuses on organisms ordinarily too small to be seen without magnification.

Put these in usual order from largest to smallest: helminth, protozoan, bacterium, virus, prion.

Helminth > protozoan > bacterium > virus > prion.

How do prokaryotes differ from eukaryotes?

Prokaryotes lack a true nucleus and membrane-bound organelles. Eukaryotes have a true nucleus and membrane-bound organelles.

Which domains are prokaryotic?

Bacteria and Archaea.

How do bacteria and archaea differ from eukaryotes at a high level?

They are usually single-celled, lack a nucleus and membrane-bound organelles, and have different cell-wall chemistry. Archaea are distinct from bacteria.

Why are microbes important to Earth?

They have shaped Earth's habitats for billions of years, recycle matter, influence atmospheric chemistry, support food webs, and affect human health.

Why is evolution called a scientific theory?

A scientific theory is a broad, evidence-supported explanation that has survived repeated testing. It is not a casual guess.

What is natural selection?

Individuals with heritable traits that improve survival or reproduction tend to leave more offspring, making those traits more common over generations.

What is biotechnology?

The deliberate use of organisms, cells, or biological molecules to make useful products or solve problems.

Who built the first simple microscope and observed 'animalcules'?

Antonie van Leeuwenhoek.

What major contributions did Louis Pasteur make to microbiology?

He helped disprove spontaneous generation, developed pasteurization, and linked microbes with disease.

What major contribution did Robert Koch make to microbiology?

He showed that Bacillus anthracis causes anthrax and developed Koch's postulates to connect a microbe with a disease.

What is the germ theory of disease?

The idea that many diseases are caused by microorganisms that invade and multiply in a host.

What are the four main families of biological macromolecules?

Carbohydrates, lipids, proteins, and nucleic acids.

What is the difference between a monomer and a polymer?

A monomer is a small subunit. A polymer is a chain of monomers.

What are the major roles of carbohydrates in cells?

They provide energy, participate in metabolic reactions, and form structural or storage polysaccharides.

Give examples of important polysaccharides and one role for each.

Starch and glycogen store energy; cellulose supports plant/algal cell walls; chitin supports fungal cell walls; peptidoglycan supports bacterial cell walls.

What are the main functions of lipids?

They store energy and form membranes. Important examples include triglycerides, phospholipids, waxes, and steroids.

What are proteins made of, and what do they do?

Proteins are chains of amino acids. They act as enzymes and as structural, transport, signaling, membrane, ribosomal, and immune components.

What are the four levels of protein structure?

Primary: amino-acid sequence. Secondary: local folding such as alpha helices or beta sheets. Tertiary: full 3D shape of one polypeptide. Quaternary: arrangement of multiple polypeptide subunits.

What are the three components of a nucleotide?

A pentose sugar, a phosphate group, and a nitrogenous base.

How do DNA and RNA differ?

DNA contains deoxyribose and thymine. RNA contains ribose and uracil. Both use adenine, guanine, and cytosine.

What are the three components of ATP?

Adenine, ribose, and three phosphate groups.

Name three characteristics common to all cells.

A plasma membrane, cytoplasm, ribosomes, and genetic material are common to all cells. Any three earn the point.

What major molecule forms the basic framework of cell membranes?

Phospholipids.

What are the Five I's of microbiology?

Inoculation, incubation, isolation, inspection, and identification.

What is inoculation?

Introducing an inoculum, a small sample of microbes, into a culture medium.

What is incubation?

Providing controlled conditions, such as temperature and atmosphere, that allow inoculated microbes to grow.

What is isolation?

Separating one microbe from a mixed culture to obtain a pure culture.

What is inspection in the Five I's?

Observing cultures macroscopically and microscopically, often with staining.

What is identification in the Five I's?

Determining the identity of an isolate, often to species level, using traits such as morphology, biochemical tests, immunologic tests, or genetic analysis.

What is a culture medium?

A nutrient preparation used to grow microorganisms in the laboratory.

What is an inoculum?

A small sample of microorganisms introduced into a medium to begin a culture.

What are the three physical states of culture media?

Liquid broth, semisolid medium, and solid medium.

When is liquid broth especially useful?

For growing large numbers of organisms, observing diffuse growth, or testing some biochemical reactions.

When is semisolid medium especially useful?

It is useful for testing motility and some oxygen or growth-pattern requirements.

When is solid agar medium especially useful?

For isolating colonies, observing colony morphology, counting viable cells, and performing many diagnostic tests.

What is agar, and why is it used in culture media?

Agar is a seaweed-derived solidifying agent. It stays solid at incubation temperatures and usually is not digested by most microbes.

How does defined medium differ from complex medium?

Defined medium has a known chemical composition. Complex medium contains ingredients such as extracts or digests whose exact chemical composition is not fully known.

What is selective medium?

A medium that inhibits some microbes while permitting or favoring growth of selected microbes.

What is differential medium?

A medium that allows multiple microbes to grow but reveals visible differences based on biochemical reactions or traits.

What is enrichment medium?

A medium designed to increase the numbers of a desired microbe that is initially present in low abundance.

What is a colony?

A visible cluster of cells on solid medium that usually arose from one cell or a small group of identical cells.

Why is aseptic technique used in microbiology?

To prevent contamination of the culture, the environment, and the worker.

How do millimeters, micrometers, and nanometers compare?

1 mm = 10^-3 m, 1 µm = 10^-6 m, and 1 nm = 10^-9 m.

What are the three elements of good microscopy?

Magnification, resolution, and contrast.

What is magnification?

The degree to which an image is enlarged compared with the actual object.

What is resolution?

The ability to distinguish two close points as separate objects.

What is contrast?

The visible difference between a specimen and its background.

How do light microscopy and electron microscopy differ?

Light microscopy uses visible light and glass lenses. Electron microscopy uses electrons and electromagnetic lenses, providing much higher resolution.

What is the difference between TEM and SEM?

TEM passes electrons through a specimen to show internal details. SEM scans a specimen's surface to show three-dimensional surface detail.

What is a simple stain used for?

It uses one dye to reveal basic cell shape, size, and arrangement.

What is a differential stain used for?

It uses multiple reagents to distinguish different groups of cells, such as Gram-positive versus Gram-negative cells.

Name three commonly used special stains.

Capsule stain, endospore stain, and flagellar stain.

What does the Gram stain primarily distinguish?

Differences in bacterial cell-envelope structure, especially thick peptidoglycan Gram-positive cells versus thin peptidoglycan Gram-negative cells.

What structures do all bacterial cells possess?

Cytoplasmic membrane, cytoplasm, ribosomes, cytoskeleton, and one or a few chromosomes.

What structures are found in some, but not all, bacteria?

Flagella, pili, fimbriae, outer membrane, nanotubes/nanowires, plasmids, inclusions, endospores, and microcompartments.

How do bacteria and archaea differ from eukaryotes?

They lack a true nucleus and membrane-bound organelles. Their DNA packaging and cell-wall chemistry also differ from eukaryotes.

What are the three major bacterial shapes?

Cocci, bacilli or rods, and spiral or corkscrew forms.

What does pleomorphism mean?

Variation in cell shape or cell-wall structure within a bacterial population, often due to genetic or nutritional differences.

Name common bacterial arrangements.

Single cells, diplo- pairs, strepto- chains, staphylo- clusters, tetrads, and sarcinae packets.

What is the glycocalyx?

An outer polysaccharide-rich coating that can appear as a capsule, slime layer, or fiber network and can aid protection, adherence, and signaling.

How does a capsule differ from a slime layer?

A capsule is organized and firmly attached. A slime layer is diffuse, loosely attached, and more easily removed.

What is a biofilm?

A structured microbial community attached to a surface and embedded in a self-produced matrix.

Why are biofilms clinically important?

They promote attachment, persistence, and resistance to host defenses and antimicrobial treatment, especially on devices and tissues.

What is the main function of bacterial flagella?

Motility.

What are the three structural parts of a bacterial flagellum?

Filament, hook, and basal body.

What is chemotaxis?

Directed movement toward or away from a chemical stimulus.

What are periplasmic flagella or axial filaments?

Internal flagella in spirochetes located between the cytoplasmic membrane and cell wall; they produce corkscrew-like movement.

How do fimbriae and pili differ?

Fimbriae mainly support attachment. Pili are longer and fewer; many are involved in conjugation or specialized attachment/motility roles.

What is the main role of a conjugation pilus?

To help transfer genetic material between bacterial cells.

What layers can make up the bacterial cell envelope?

Cytoplasmic membrane, cell wall, and in some bacteria an outer membrane.

What is peptidoglycan?

A strong mesh-like polymer in bacterial cell walls that provides shape and resists osmotic pressure.

How does a Gram-positive cell wall differ from a Gram-negative cell wall?

Gram-positive cells have thick peptidoglycan and no outer membrane. Gram-negative cells have thin peptidoglycan plus an outer membrane.

Why do Gram-positive bacteria appear purple after Gram staining?

Their thick peptidoglycan retains the crystal violet-iodine complex during decolorization.

Why do Gram-negative bacteria appear pink or red after Gram staining?

Their thin peptidoglycan does not retain crystal violet after decolorization, so they take up the counterstain.

What is lipopolysaccharide, LPS, and why is it important?

LPS is a component of the Gram-negative outer membrane. Its lipid portion acts as endotoxin and can contribute to fever and shock.

What are porins?

Protein channels in the Gram-negative outer membrane that allow selected chemicals to enter.

What is the bacterial nucleoid?

The irregular region of cytoplasm containing the bacterial chromosome; it is not enclosed by a nuclear membrane.

What is a plasmid?

A small, usually circular DNA molecule separate from the chromosome that can carry accessory genes such as antimicrobial resistance genes.

What is an endospore?

A dormant, highly resistant survival structure formed by some bacteria under unfavorable conditions. It is not a reproductive structure.

What triggers endospore formation?

Adverse conditions, especially nutrient depletion or other environmental stress.

What feature defines a eukaryotic cell?

A true nucleus enclosed by a membrane, along with membrane-bound organelles.

How do eukaryotic flagella differ from bacterial flagella?

Eukaryotic flagella are thicker, membrane-covered, and contain microtubules in a 9 + 2 arrangement. Bacterial flagella are simpler protein filaments driven by rotation.

How do cilia compare with eukaryotic flagella?

Cilia have the same 9 + 2 microtubule pattern but are shorter and more numerous.

What are the main components of a eukaryotic nucleus?

Nuclear envelope, pores, nucleoplasm, chromatin or chromosomes, and nucleolus.

What is the function of the nucleolus?

It synthesizes rRNA and assembles ribosomal subunits.

How do rough ER and smooth ER differ?

Rough ER has attached ribosomes and helps process/transport proteins. Smooth ER lacks ribosomes and is involved in lipid synthesis, storage, and nutrient processing.

What is the main function of the Golgi apparatus?

It modifies, sorts, packages, and distributes molecules in vesicles.

Trace the secretory pathway for a protein made for export.

Nucleus instructions → ribosomes on rough ER → transport vesicles → Golgi apparatus → secretory vesicles → cell membrane/exterior.

What is the primary function of mitochondria?

They generate ATP through aerobic cellular respiration.

What evidence supports the endosymbiotic origin of mitochondria?

Mitochondria divide independently, contain circular DNA, and have bacteria-sized 70S ribosomes.

How do eukaryotic and bacterial ribosomes differ?

Eukaryotic cytoplasmic ribosomes are 80S, made of 60S and 40S subunits. Bacterial ribosomes are 70S, made of 50S and 30S subunits.

What are the three main cytoskeletal fiber types?

Microfilaments, intermediate filaments, and microtubules.

What are microfilaments primarily made of and what do they help with?

Actin; they help with cell shape, movement, and contraction.

What are microtubules primarily made of and what do they help with?

Tubulin; they help with intracellular transport, cell division, and flagella/cilia structure.

What are fungi?

Eukaryotic, chemoheterotrophic organisms that absorb nutrients and usually have rigid cell walls containing chitin and other polysaccharides.

How do yeasts and molds differ?

Yeasts are usually unicellular. Molds are multicellular filamentous fungi made of hyphae.