MICR3050 Clemson

What is a microorganism?

An organism or acellular biological entity too small to be clearly seen with the unaided eye; the lecture gives a general cutoff of about ≤1 mm and notes that many are unicellular.

Which major cellular groups are studied by microbiologists?

Fungi, protists, Bacteria, and Archaea.

Which major acellular entities are studied by microbiologists?

Viruses, viroids/virusoids/satellites, and prions.

What does 'acellular' mean?

Lacking cellular organization; it does not mean that the entity lacks biological macromolecules.

What are the basic characteristics of viruses?

Acellular; contain a DNA or RNA genome inside a protein capsid, sometimes with a lipid envelope; lack ribosomes and independent metabolism; replicate only inside suitable host cells.

What is a viroid?

A small infectious RNA molecule, classically associated with plant disease.

What is a prion?

An infectious misfolded protein.

Why is 'microorganism' a practical category rather than a statement that every member is alive?

Because microbiologists study both cellular organisms and acellular infectious entities such as viruses, viroids, and prions.

What is the key structural distinction between prokaryotic and eukaryotic cells?

Prokaryotic cells lack a membrane-bound nucleus; eukaryotic cells have a membrane-bound nucleus and membrane-bound organelles.

Which domains have prokaryotic cellular organization?

Bacteria and Archaea.

Which domain contains eukaryotic cells?

Eukarya.

Where is DNA located in a typical prokaryotic cell?

In a nucleoid region rather than inside a membrane-bound nucleus.

What is the typical ribosome pattern in prokaryotic cytoplasm?

70S ribosomes.

What is the typical ribosome pattern in eukaryotic cytoplasm?

80S ribosomes; mitochondria and chloroplasts contain bacterial-like ribosomes.

Why is the term 'prokaryote' considered evolutionarily controversial?

Bacteria and Archaea are deeply distinct evolutionary domains, so 'prokaryote' is useful structurally but does not describe one evolutionary branch equivalent to Eukarya.

What are examples of eukaryotic microbes?

Protists such as algae, protozoa, slime molds, and water molds, plus fungi such as yeasts and molds.

What are examples of prokaryotic microbes?

Bacteria such as E. coli and Archaea such as methanogens.

Which four properties are shown as properties of all cells in the lecture?

Structure, metabolism, growth, and evolution.

Which four properties are shown as properties of some cells in the lecture?

Differentiation, communication, motility, and horizontal gene transfer.

What basic structures provide cellular organization in all cells?

A cytoplasmic membrane, cytoplasm, a genome, and ribosomes.

What is metabolism?

The set of chemical reactions by which cells obtain and transform nutrients, conserve energy, and synthesize cell material.

What is catabolism?

Metabolic reactions that break down molecules and release usable energy.

What is anabolism?

Metabolic reactions that build macromolecules and other cell components.

What does microbial growth usually mean?

An increase in cell number or population size as nutrients are converted into new cell material.

How does evolution occur in microbial populations?

Heritable DNA changes create variation, and natural selection changes genotype frequencies over generations.

What is cellular differentiation?

Formation of specialized cell types or structures, such as spores, by some microorganisms.

What is microbial communication?

Chemical signaling between cells that coordinates behavior, such as quorum sensing.

What is motility?

Self-propelled movement, often using structures such as flagella or pili.

What is horizontal gene transfer?

Movement of DNA between cells in the same generation rather than from parent to offspring.

What are three major mechanisms of horizontal gene transfer?

Transformation, transduction, and conjugation.

What is a coccus?

A spherical bacterial cell; plural: cocci.

What are diplococci?

Pairs of cocci.

What are streptococci?

Chains of cocci.

What are staphylococci?

Irregular grape-like clusters of cocci.

What are tetrads?

Groups of four cocci, commonly produced by division in two perpendicular planes with incomplete separation.

What are sarcinae?

Cubical packets of cocci, commonly groups of eight or multiples of eight, produced by division in three perpendicular planes.

What is a bacillus?

A rod-shaped bacterial cell; plural: bacilli.

What are coccobacilli?

Very short rods.

What are vibrios?

Curved or comma-shaped rods.

What are spirilla?

Rigid helical cells.

What are spirochetes?

Flexible helical cells.

What does filamentous morphology mean?

Cells grow as long filaments.

What is a mycelium in microbial morphology?

A network or mass of long filaments.

What does pleomorphic mean?

Variable in shape.

What unusual shapes can Archaea have?

Pleomorphic, branched, flat, square, and other unusual forms.

What determines bacterial cell arrangement after division?

The plane or planes of division and how completely daughter cells separate.

What size range does the lecture list for eukaryotic cells?

About 0.8 µm to hundreds of micrometers.

What size range does the lecture list for Bacteria and Archaea?

About 0.2 µm to 750 µm.

What size range does the lecture list for viruses?

About 0.01 µm to 1 µm.

How does surface area scale with linear cell size?

Surface area scales approximately with length squared.

How does volume scale with linear cell size?

Volume scales approximately with length cubed.

What happens to surface area-to-volume ratio as a cell gets larger?

It decreases because volume grows faster than surface area.

For a sphere, what is the relationship between SA:V and radius?

SA:V = 3/r, so increasing radius lowers SA:V.

What SA:V values are given in the lecture for spheres with r = 1 µm and r = 2 µm?

r = 1 µm gives SA:V = 3; r = 2 µm gives SA:V = 1.5.

Why can small cell size be advantageous?

Small cells have a high SA:V, giving more membrane area relative to cytoplasm for nutrient uptake, waste removal, gas exchange, sensing, and transport.

What additional intracellular advantage comes with small cell size?

Short diffusion distances within the cell can support rapid access to resources and quick responses.

Does small size automatically mean a cell is always more metabolically active?

No. The key tested idea is the physical transport advantage created by a higher SA:V.

What molecular comparison was used to develop the Universal Phylogenetic Tree?

DNA sequences encoding small-subunit ribosomal RNA (SSU rRNA).

What are the basic steps for using SSU rRNA genes to infer a phylogenetic tree?

Isolate DNA, amplify/copy the rRNA gene, sequence it, align homologous sequences, compare differences, and infer evolutionary relationships.

What are the three domains of life?

Bacteria, Archaea, and Eukarya.

What does LUCA stand for?

Last Universal Common Ancestor.

What is LUCA?

The ancestral cellular population from which the three domains ultimately descended.

Which two domains share a more recent common ancestor with each other in the lecture tree?

Archaea and Eukarya.

What is a major structural hallmark of Bacteria emphasized in this unit?

Peptidoglycan in the bacterial cell wall.

How do Archaea differ from Bacteria despite both being prokaryotic?

Archaea have distinctive membrane lipids and molecular machinery and lack bacterial peptidoglycan.

How do mutations contribute to microbial evolution?

They change genetic material and create new genotypes.

How can genetic changes affect phenotype?

Some mutations or acquired genes alter observable traits or functions.

What is natural selection?

The increase in frequency of advantageous heritable traits when they improve survival or reproduction in a given environment.

How can horizontal gene transfer accelerate microbial evolution?

It introduces new genes and capabilities, such as metabolic traits or antimicrobial resistance, within the same generation.

Do individual microbial cells evolve because they need to?

No. Variation arises first; natural selection changes genotype frequencies in populations over time.

How does the lecture define a microbial species?

A collection of strains that share many stable properties and differ significantly from other groups of strains.

Why is 'microbial species' called a controversial term?

Microbes do not always fit the classical reproductive species concept, and horizontal gene transfer can blur boundaries.

What is a microbial strain?

The descendants of a single pure microbial culture; a strain is a subset of a microbial species.

What is a type strain?

A designated reference strain used to represent a microbial species.

What kinds of traits can differ among strains of the same species?

Virulence, antigenic profile, nutrient use, drug susceptibility, toxin production, and genome content.

What is binomial nomenclature?

A two-part scientific name consisting of Genus + species.

How should a microbial scientific name be written?

Genus capitalized, species lowercase, both italicized when typed; after first use the genus may be abbreviated if unambiguous, e.g., E. coli.

Why are microorganisms important in Earth's history?

They are the oldest forms of life and among the most abundant and diverse organisms.

Approximately how many microbial cells does the lecture estimate exist?

About 2 × 10^30 microbial cells.

Where are microorganisms found?

In nearly every environment where life can exist.

What role do microbes play in biogeochemical cycles?

They recycle essential elements and act as major reservoirs and transformers of nutrients.

What role do photosynthetic microbes play?

They contribute to primary production by converting light energy into chemical energy.

How do microbes affect other living organisms?

Most interactions are beneficial or benign, some are harmful, and many organisms depend on microbes for normal ecosystem or host functions.

What major areas of human life are influenced by microbes?

Disease, normal microbiota, food production, agriculture, energy, environment, and industrial processes.

Why are microbes useful experimental model systems?

Many grow rapidly and are easy to study genetically and biochemically.

What did Robert Hooke contribute to microbiology?

In 1665 he used early microscopy and described fruiting structures of molds.

What did Antony van Leeuwenhoek contribute to microbiology?

From 1674-1676 he was the first to accurately observe and describe bacteria.

What did Francesco Redi contribute to the spontaneous-generation debate?

In 1668 he used meat in open, sealed, and gauze-covered jars to show that maggots came from flies, not from the meat itself.

What did Louis Pasteur's swan-neck flask experiment show?

Sterile broth remained free of growth when air could enter but dust and microbes were trapped, disproving spontaneous generation.

What key control logic made Pasteur's swan-neck flask experiment convincing?

Air was still allowed into the flask, so lack of growth could not be explained by excluding air or a supposed 'vital force.'

What did Louis Pasteur show about fermentation?

He demonstrated that microorganisms carry out fermentations.

What is pasteurization?

A process developed by Pasteur that uses controlled heating to reduce microbial spoilage/pathogens without full sterilization.

What is attenuation?

Loss or reduction of a pathogen's ability to cause disease, which can allow use in vaccines.

Which vaccines are associated with Pasteur and coworkers in the lecture?

Vaccines for chicken cholera, anthrax, and rabies.

What did Ignaz Semmelweis demonstrate?

Handwashing reduced puerperal or 'childbed' fever.

What did Joseph Lister contribute?

He developed antiseptic surgical practices designed to prevent microbes from entering wounds, reducing postoperative infections.

What did Robert Koch establish?

A causal relationship between specific microorganisms and specific diseases, including Bacillus anthracis and anthrax, and the criteria now called Koch's postulates.

What laboratory advances are associated with Koch's work?

Agar, Petri dishes, nutrient broth/agar, and methods for isolating microorganisms such as streak plating.

What did Alexander Fleming discover?

Penicillin in 1929.

What did Edward Jenner contribute?

Vaccination against smallpox.