Exam 1 BIO 260

Size of a Virus

20–200 nm

Size of a Bacteria

1–10 µm

Size of an Eukaryote

10-100µm

Size of a Prokaryote

1-10µm

What phenotypic characteristics are used to classify microorganisms?

• Size

• Shape

• Structures

• Ability

How is 16S rRNA used to identify/classify microorganisms?

By comparing its gene sequence among organisms to infer evolutionary relationships

Why is 16S rRNA ideal for identifying prokaryotes?

It's highly conserved, present in all prokaryotes, contains variable regions, and rarely undergoes horizontal gene transfer (most important reason).

What are the three domains of life?

Bacteria, Archaea, Eukarya.

Define the endosymbiotic theory.

Theory that mitochondria and chloroplasts originated as free-living prokaryotes engulfed by ancestral eukaryotic cells.

What evidence supports the endosymbiotic theory?

Mitochondria/chloroplasts have circular DNA, ribosomes similar to bacteria, reproduce independently via binary fission.

How do you classify an organism into the correct domain?

Based on cellular structure, presence of membrane-bound organelles, type of ribosomes, etc.

What are characteristics common to all domains?

DNA as genetic material, ribosomes, cytoplasm, cell membrane, reproduction.

What are unique traits of each domain?

• Bacteria: Peptidoglycan cell wall

• Archaea: Unique lipids, extremophiles

• Eukarya: Membrane-bound organelles

Name and describe a non-living microbe.

Viruses—acellular, need a host to replicate, made of genetic material and a protein coat.

Difference between genus, species, strain?

• Genus: Group of related species

• Species: Basic unit of classification

• Strain: Genetic variant within a species

How do you write microbial names using Binomial Nomenclature?

Genus species (italicized or underline, Genus capitalized, species lowercase), e.g., Escherichia coli

What are the steps in the chain of infection (in order)?

1. Infectious agent

2. Reservoir

3. Portal of exit

4. Mode of transmission

5. Portal of entry

6. Susceptible host

What are the three types of reservoirs of infection?

• Human (e.g. carriers)

• Animal (zoonoses)

• Environmental (soil, water)

What is a zoonotic disease?

A disease that originates in animals and is transmitted to humans.

How do diseases enter and exit the body?

Through portals such as skin, mucous membranes, respiratory tract, GI tract, etc.

What are the modes of disease transmission?

• Direct (contact, droplet)

• Indirect (fomites, airborne, vector)

Common disease vectors?

Mosquitoes, ticks, fleas.

How can communicable diseases be controlled?

Isolation, vaccination, hygiene, vector control, disinfecting reservoirs, blocking portals.

Key differences between prokaryotic and eukaryotic cells?

• Prokaryotes: No nucleus, no membrane-bound organelles, circular DNA

• Eukaryotes: Nucleus, membrane-bound organelles, linear DNA

What prokaryotic features are in all cells?

Plasma membrane, cytoplasm, ribosomes, DNA.

How do Gram+ and Gram– bacteria differ in cell wall structure?

• Gram+: Thick peptidoglycan, teichoic acids

• Gram–: Thin peptidoglycan, outer membrane with LPS

Unique structures in Gram+ and Gram– bacteria?

• Gram+: Teichoic acids

• Gram–: Outer membrane, lipopolysaccharide (LPS), porins

Final stain colors after Gram staining?

• Gram+: Purple

• Gram–: Pink/red

How do lysozyme and penicillin damage bacteria?

• Lysozyme: Breaks glycosidic bonds in peptidoglycan

• Penicillin: Inhibits cross-linking of peptidoglycan

Basic structure of the cell membrane?

Phospholipid bilayer with embedded proteins; semi-permeable.

Internal bacterial structures and their functions?

• Cytoplasm: Fluid for metabolic activity

• Ribosomes: Protein synthesis

• Nucleoid: DNA region

• Plasmids: Extra-chromosomal DNA

• Storage granules/inclusions: Nutrient reserves

• Endospores: Dormant, resistant survival structures

External bacterial structures and their functions?

• Flagella: Motility

• Pili: DNA transfer (conjugation)

• Fimbriae: Attachment

• Glycocalyx: Protection, adherence (capsule or slime layer)

What are the four biosafety levels?

• BSL-1: Non-pathogenic microbes

• BSL-2: Moderate risk, disease in humans

• BSL-3: Serious disease via inhalation

• BSL-4: High risk, life-threatening diseases

What PPE and safety practices are required for each biosafety level?

• BSL-1: Standard lab coat, gloves, basic hygiene

• BSL-2: Lab coat, gloves, eye protection, biohazard signage

• BSL-3: Respirators, controlled access, specialized ventilation

• BSL-4: Full-body positive pressure suits, isolated facilities

Name different portals of entry and exit for pathogens.

Skin, respiratory tract, GI tract, urogenital tract, conjunctiva, blood.

List and describe modes of transmission:

• Direct contact: Physical touch

• Droplet transmission: Short-range respiratory droplets

• Airborne: Inhalation of small particles

• Fomite (indirect): Contaminated objects

• Vector-borne: Carried by insects or animals

How can communicable diseases be controlled?

• Isolating infected individuals

• Vaccination

• Proper hygiene and sanitation

• Vector control

• Safe food and water handling

• Protective equipment

Compare and contrast prokaryotic and eukaryotic cells.

• Prokaryotes: No nucleus, no membrane-bound organelles, smaller size, circular DNA, 70S ribosomes.

• Eukaryotes: Nucleus, organelles, larger size, linear DNA, 80S ribosomes.

Structure & function of the eukaryotic cell membrane?

Phospholipid bilayer, semi-permeable, regulates movement of substances in/out of cell.

Structure & function of the nucleus?

Contains DNA, site of transcription, surrounded by nuclear envelope.

Structure & function of mitochondria?

Double membrane, own DNA, site of ATP production via cellular respiration.

Structure & function of chloroplasts?

Double membrane, own DNA, perform photosynthesis.

Structure & function of rough ER?

Ribosome-covered membrane network, synthesizes proteins for secretion or membrane insertion.

Structure & function of smooth ER?

Lacks ribosomes, lipid synthesis, detoxification.

Structure & function of Golgi body?

Modifies, packages, and ships proteins and lipids.

Structure & function of lysosomes?

Membrane-bound vesicles with digestive enzymes, break down waste.

Structure & function of ribosomes?

Protein synthesis; free in cytoplasm or bound to rough ER (in eukaryotes).

Structure & function of cytoskeleton?

Network of protein filaments; supports cell shape, movement, intracellular transport.

Which features are found in all prokaryotic cells?

Cell membrane, cytoplasm, ribosomes, DNA.

Which features are optional in prokaryotic cells?

Capsule, flagella, pili, plasmids, endospores, inclusions.

Structure & function of bacterial flagella?

Long, whip-like structure for motility, made of flagellin.

Structure & function of fimbriae?

Short, hair-like, for adhesion to surfaces.

Structure & function of pili?

Longer than fimbriae, used for DNA transfer (conjugation).

Structure & function of glycocalyx?

Polysaccharide layer (capsule/slime layer); protects bacteria, aids adhesion, immune evasion.

Describe the Fluid Mosaic model of cell membranes.

Phospholipid bilayer with embedded proteins, fluid and dynamic structure allowing lateral movement.

How does lysozyme damage bacteria?

Breaks bonds in peptidoglycan, weakening the cell wall.

Define “sterile.”

Free of all living organisms, including microbes and spores.

Define “aseptic technique.”

Procedures to prevent contamination of cultures, equipment, and the environment.

Give two ways experiments are kept aseptic:

• Sterilizing media and tools before use (e.g. autoclaving, flaming loops).

• Working near a flame or in a biosafety cabinet to reduce airborne contamination.

Importance of aseptic technique?

Prevents contamination, ensures valid results, protects lab personnel and environment.

How to obtain a pure culture from a mixed sample?

• Flame sterilize loop.

• Pick a small sample from mixed culture.

• Streak on agar plate to isolate single colonies.

• From isolated colony, perform quadrant streak for purity.

How to perform a quadrant streak?

• Sterilize loop.

• Streak in first quadrant.

• Flame loop.

• Drag from quadrant 1 into quadrant 2.

• Repeat flaming and streaking into quadrants 3 and 4, thinning out bacteria to isolate colonies.

How does DNA replication differ between eukaryotic and prokaryotic cells?

• Prokaryotes: Single circular chromosome, one origin of replication, occurs in cytoplasm.

• Eukaryotes: Linear chromosomes, multiple origins of replication, occurs in nucleus.

How does transcription differ between eukaryotes and prokaryotes?

• Prokaryotes: Occurs in cytoplasm, no introns, single RNA polymerase, sigma factors help RNA polymerase bind promoters, transcription and translation coupled.

• Eukaryotes: Occurs in nucleus, introns/exons present, multiple RNA polymerases, transcription factors replace sigma factors, mRNA requires processing (capping, poly-A tail, splicing).

How does translation differ between eukaryotes and prokaryotes?

• Prokaryotes: Translation starts while mRNA is still being transcribed (coupled), occurs in cytoplasm, ribosome binds directly to ribosome-binding site.

• Eukaryotes: Translation starts after mRNA leaves nucleus, ribosomes bind to 5’ cap, occurs in cytoplasm.

What is an operon and what’s its role in gene expression?

A cluster of genes under control of one promoter, transcribed together into a single mRNA, allowing coordinated regulation of related genes.

How do you transcribe and translate a DNA sequence given a codon table?

• Replace A→U, T→A, G→C, C→G for transcription (if DNA coding strand is given).

• Read mRNA codons in sets of three to translate to amino acids using codon table.

Compare constitutive, inducible, and repressible genes.

• Constitutive genes: Always expressed (housekeeping).

• Inducible genes: Normally off, turned on in response to a molecule (inducer).

• Repressible genes: Normally on, turned off when end product accumulates.

Using the lac operon, explain the role of inducers and repressors.

• Inducer (allolactose): Binds repressor, causing it to fall off operator, allowing transcription.

• Repressor: Binds operator to block RNA polymerase when lactose absent.

Using the lac operon, explain the role of inducers and activators.

• Inducer: Allolactose removes repressor.

• Activator (CAP-cAMP): Enhances RNA polymerase binding to promoter when glucose is low.

Explain carbon catabolite repression in the lac operon.

When glucose is high, cAMP levels drop, CAP doesn’t bind promoter → lac operon not activated even if lactose is present → bacteria prefer glucose.

How to identify inducers, repressors, activators, operators, and promoters in other operons?

• Inducer: Molecule that removes repressor or activates transcription.

• Repressor: Protein that binds operator to block transcription.

• Activator: Protein that helps RNA polymerase bind promoter.

• Operator: DNA sequence repressor binds.

• Promoter: DNA sequence where RNA polymerase binds to start transcription.

List the steps and reagents of the Gram stain in order.

1. Crystal violet (primary stain)

2. Iodine (mordant)

3. Alcohol/acetone (decolorizer)

4. Safranin (counterstain)

Why do Gram+ and Gram– bacteria appear different colors at each Gram stain step?

• Crystal violet: Both purple.

• Iodine: Complexes form, both remain purple.

• Alcohol:

  • Gram+: Cell wall retains crystal violet-iodine complex → stays purple.

  • Gram–: Outer membrane dissolved, dye washes out → colorless.

• Safranin:

  • Gram+: Still purple, dye masked by crystal violet.

  • Gram–: Stains pink/red.

Define resolution in microscopy.

Ability to distinguish two points as separate objects.

Define magnification in microscopy.

How much larger the object appears compared to real size.

What happens if you increase magnification without improving resolution?

Image appears bigger but blurry—no extra detail seen.

How to prepare a bacterial smear from solid media?

• Place drop of water on slide.

• Transfer small colony, mix into water.

• Spread thin film, air dry.

• Heat-fix by passing slide through flame.

How to prepare a smear from liquid culture?

• Place loopful of liquid culture directly on slide.

• Spread into thin film.

• Air dry, heat-fix.

How to identify bacterial shape and arrangement under microscope?

• Shapes: Cocci (spheres), bacilli (rods), spirilla (spirals).

• Arrangements: Chains (strepto-), clusters (staphylo-), pairs (diplo-), singles.

Where can microorganisms be found?

Almost everywhere: soil, water, air, extreme environments, plants, animals, human body surfaces and internal tracts.

Are most microorganisms harmful or beneficial?

Most are beneficial or neutral; only a minority cause disease.

What roles do microbes play in ecosystems?

Decomposition, nutrient cycling, oxygen production, bioremediation, symbiotic relationships with plants and animals.

How do microbes participate in bioremediation?

Break down pollutants and toxic wastes into less harmful substances.

Microbial roles in decomposition?

Break down dead organisms, recycling nutrients into the ecosystem.

Microbial roles in agriculture?

Nitrogen fixation, plant growth promotion, pest control.

Microbial roles in nutrient cycling?

Cycle elements like carbon, nitrogen, sulfur, phosphorus through ecosystems.

List ways humans use microbes and their products.

• Food & beverages: yogurt, cheese, beer, bread.

• Medicine: antibiotics, vaccines, enzymes.

• Agriculture: biofertilizers, biopesticides.

• Industry: fermentation, bioplastics.

Roles of microbiota in a healthy human body?

• Compete with pathogens

• Aid digestion

• Produce vitamins (e.g. K, B12)

• Train immune system

How can microbes cause disease?

Invade tissues, produce toxins, evade immune system.

Define symbiosis.

Close, long-term relationship between different species.

Define commensalism.

One organism benefits; the other is unaffected.

Define mutualism.

Both organisms benefit.

Define parasitism.

One organism benefits at the expense of the other.

Define microbiota.

Microorganisms normally living on/in the body.

Define microbiome.

All genes and genomes of the microbiota.

Define infection.

Microbes enter and multiply in host tissue.

Define pathogen.

Microorganism that causes disease.

Define opportunist (opportunistic pathogen).

Causes disease only when host defenses are compromised.

Define emerging pathogen.

New pathogen or newly recognized disease.