Chapter 03 Lecture Notes: Nester's Microbiology — Prokaryotic vs Eukaryotic Cells, Gram Stain, Cell Structures, and Microscopy

A comprehensive set of Q&A flashcards covering Gram staining, prokaryotic and eukaryotic cell structures, and microscopy concepts from the lecture notes.

What are the two major groups of bacteria identified by the Gram stain?

Gram-positive and Gram-negative.

What determines Gram-positive vs Gram-negative classification?

Cell wall structure and chemistry.

What are the two fundamental cell types in biology?

Prokaryotic and eukaryotic cells.

Why are differences between prokaryotic and eukaryotic cells clinically important?

Bacterial components are targets for antibacterial medications that selectively affect bacteria.

What is the typical size relationship between prokaryotic and eukaryotic cells?

Prokaryotic cells are generally smaller.

What is the significance of the high surface-area-to-volume ratio in prokaryotes?

Facilitates nutrient uptake and waste excretion, but increases vulnerability to threats.

What is the cytoplasmic membrane composed of?

Phospholipid bilayer embedded with proteins.

What does the Fluid Mosaic Model describe?

Membrane structure where proteins drift within a phospholipid bilayer.

How do archaeal membranes differ from bacterial membranes?

Archaea have lipid tails not made of fatty acids and are connected differently to glycerol; distinct phospholipid compositions.

What is osmosis?

Diffusion of water across a selectively permeable membrane driven by solute differences.

What is the difference between hypotonic and hypertonic environments for cells with a wall?

Hypotonic: water enters the cell; hypertonic: water leaves; the cell wall helps prevent bursting in hypotonic environments.

What are aquaporins?

Protein channels that facilitate water movement across membranes.

What is proton motive force?

Electrochemical gradient across the cytoplasmic membrane used to synthesize ATP and drive transport.

What is simple diffusion?

Movement of molecules from high to low concentration without energy input.

What is facilitated diffusion?

Passive transport requiring transporter proteins.

What is active transport?

Movement against a concentration gradient that requires energy (can be via proton motive force or ATP).

What is a common example of active transport driven by ATP?

ABC transporters.

What is group translocation?

Chemically modifies a compound during passage through the membrane (e.g., phosphorylation during glucose uptake).

What is protein secretion?

Active movement of proteins out of the cell; proteins may have signal sequences for secretion.

What is the glycocalyx, and what structures does it include?

Gel-like layer outside the cell wall, including capsule and slime layer made of glycocalyx.

What is the difference between a capsule and a slime layer?

Capsule is distinct and gelatinous; slime layer is diffuse and irregular.

What is a biofilm?

A polymer-encased community of cells attached to a surface.

What is the function of flagella?

Motility; propel the cell; energy source differs between domains (proton motive force in bacteria; ATP in archaea).

What are the main parts of a bacterial flagellum?

Basal body, hook, filament (made of flagellin subunits).

How do archaeal flagella differ from bacterial flagella?

Archaella are structurally distinct and use ATP as an energy source.

What is chemotaxis?

Movement toward chemical attractants (nutrients) or away from toxins.

What other taxis types do bacteria exhibit besides chemotaxis?

Aerotaxis, magnetotaxis, thermotaxis, and phototaxis.

What are pili (fimbriae) and their functions?

Shorter, thinner than flagella; help attachment and, in some types, twitching/gliding motility; sex pili enable DNA transfer.

What is the nucleoid?

Gel-like region where the bacterial chromosome (single circular dsDNA) is located.

What are plasmids?

Small, extrachromosomal DNA that can be transferred between bacteria and often carry antibiotic resistance genes.

What is the 70S ribosome?

Prokaryotic ribosome composed of 30S and 50S subunits; target of many antibiotics.

What is the 80S ribosome and where is it found?

Eukaryotic ribosome composed of 60S and 40S subunits.

Why are antibiotics that target 70S ribosomes generally not harmful to humans?

Because human ribosomes are 80S, not 70S.

What is the bacterial cytoskeleton and what storage granules are common?

Interior protein framework; storage granules like glycogen, PHB, and polyphosphate.

What are metachromatic granules?

Storage granules that appear red with methylene blue staining.

What are gas vesicles and encapsulin compartments?

Gas vesicles provide buoyancy; encapsulin nanocompartments store specific proteins; both are protein-based compartments.

What are endospores and which bacteria form them?

Dormant, highly resistant cells formed by Bacillus and Clostridium.

What triggers endospore formation (sporulation) and what is its purpose?

Triggered by nutrient limitation; protects the genome during adverse conditions; not a reproductive process.

What evidence supports the endosymbiotic theory for mitochondria and chloroplasts?

DNA and ribosomes resemble bacterial 70S, double membranes, replication by binary fission, and similarity to bacteria (rickettsias and cyanobacteria).

What are chloroplasts and their role?

Sites of photosynthesis in plants and algae; contain DNA and 70S ribosomes; have outer and inner membranes.

What is the nucleus and its key features?

Membrane-bound organelle containing DNA; nuclear pores permit large molecules to pass; nucleolus synthesizes rRNA.

What are mitochondria and their primary function?

Generate ATP; possess two membranes with cristae; matrix contains DNA and 70S ribosomes.

What is the endomembrane system in eukaryotic cells?

ER (rough and smooth), Golgi apparatus, lysosomes, peroxisomes—these organelles work together to synthesize, modify, and transport proteins and lipids.

What distinguishes rough ER from smooth ER?

Rough ER has ribosomes and synthesizes proteins destined for secretion or membranes; smooth ER synthesizes lipids and stores calcium.

What is the Golgi apparatus responsible for?

Modifies, sorts, and packages macromolecules; adds carbohydrate and phosphate groups and directs vesicle transport.

What are lysosomes and peroxisomes' roles?

Lysosomes degrade material with enzymes; peroxisomes degrade lipids and detoxify chemicals using oxygen-containing reactions.

What are the main microscopy modalities mentioned and their uses?

Light microscopy (various contrasts), dark-field, phase-contrast, DIC, fluorescence; electron microscopy (TEM and SEM); scanning probe microscopy (AFM); super-resolution methods.

What is immersion oil used for in light microscopy?

Displaces air between the lens and specimen to increase numerical aperture and resolution with high-power objectives.

What is the maximum resolving power of the light microscope?

About 0.2 micrometers.

What is fluorescence microscopy used for?

Observing fluorescent or dye-tagged molecules; immunofluorescence uses fluorescent antibodies to label specific proteins.

What is confocal microscopy and its advantage?

Laser scans a plane to create sharp optical sections; computer assembles 3D images.

What is two-photon microscopy and its benefit?

Similar to confocal but uses lower energy light, causing less photodamage and enabling deeper imaging.

What is a scanning electron microscope (SEM) used for?

Imaging surface details with a beam of electrons, producing a 3D-like surface image.

What is a transmission electron microscope (TEM) used for?

Imaging internal cell structures by transmitting electrons through thin sections; very high-resolution imaging.

What are scanning probe microscopes (AFM) and what can they do?

Use a sharp probe to feel surface topography at atomic resolution; can image individual atoms.

What is a wet mount preparation?

A live specimen placed in a drop of liquid under a coverslip to observe living organisms.

What is a smear in light microscopy preparation?

Drying and fixing a specimen before staining to visualize cells.

What stains are used to visualize capsules, endospores, and flagella?

Capsule stain uses India ink; endospore stain uses malachite green with heat; flagella stain uses a dye to bind thin flagella.

What is the Gram staining sequence and its significance?

Primary stain → iodine mordant → decolorization with alcohol → counterstain; effectiveness depends on decolorization time and culture age.

What organisms are detected by the acid-fast stain and why?

Mycobacterium species with high mycolic acid content; red acid-fast cells retained after acid-alcohol decolorization.

What is the purpose of a capsule stain?

Visualizes the capsule by staining the background; capsules themselves stain poorly.

What is endospore staining and why is heat used?

Malachite green penetrates spores with heat; a counterstain colors other cells pink.

What is the purpose of flagella staining?

Adheres dye to thin flagella to visualize presence and arrangement.

What is the significance of LPS in Gram-negative bacteria?

Outer membrane endotoxin signaling the immune system; can be lethal in high amounts; contains Lipid A and O antigen.

What are teichoic acids and where are they found?

Teichoic acids extend above the peptidoglycan layer in Gram-positive cell walls.

What is the periplasmic space and where is it located?

Space between the cytoplasmic membrane and outer membrane in Gram-negative bacteria; contains gel-like periplasm and binding proteins.