Microbiology - Chapter 4 Notes

Vocabulary flashcards defining key bacterial morphology, staining methods, pathogenicity factors, host-pathogen interactions, and eukaryotic cell structures covered in Chapter 4.

Causative agent of Sydney's fatal infection in the opening case study

Neisseria meningitidis (also known as meningococcus)

Morphological and Gram-stain classification of Neisseria meningitidis

Gram-negative diplococcus

Transmission route of Neisseria meningitidis

Spread through saliva (for example, sharing or chewing on toys in daycare)

Initial cellular mechanism used by Neisseria meningitidis to infect host cells

Attaching to host cells using specialized surface molecules that vary between bacterial strains

Prophylactic antibiotic administered to contacts exposed to Neisseria meningitidis

Rifampicin

Key structural difference defining prokaryotes versus eukaryotes

Prokaryotes lack a true nucleus and membrane-enclosed organelles, whereas eukaryotes possess a membrane-enclosed nucleus and internal organelles.

Standard biological convention for writing an organism's genus and species name

Italicized with the genus name capitalized and the specific name in lower case (for example, Homo sapiens).

Taxonomic gene sequence used to define species classification in prokaryotes

The $16S$ ribosomal RNA ($16S$ rRNA) gene sequence

Meaning of the term pleomorphic in bacterial morphology

The capability of certain bacteria to alter or change their shape.

Typical size range of human-colonizing or pathogenic bacteria

$0.1\,\mu\text{m}$ to $10\,\mu\text{m}$ in their largest dimension

Typical size range of standard viral particles versus giant viruses

Standard viruses range from $30\,\text{nm}$ to $300\,\text{nm}$ ($0.03\,\mu\text{m}$ to $0.3\,\mu\text{m}$), while Megaviridae reach up to $1\,\mu\text{m}$.

Typical size range of protozoa and fungi

$4\,\mu\text{m}$ to $40\,\mu\text{m}$

Limit of resolution for the human eye, light microscope, and electron microscope

Human eye: $40\,\mu\text{m}$; Light microscope: $0.2\,\mu\text{m}$; Electron microscope: $0.003\,\mu\text{m}$.

Morphological term for spherical or ovoid bacterial cells

Cocci (singular: coccus)

Morphological term for straight rod-shaped bacterial cells

Bacilli (singular: bacillus)

Morphological term for extremely short rod-shaped bacterial cells

Coccobacilli

Morphological term for rod-shaped bacterial cells with tapered ends

Fusiform bacilli

Morphological term for rigid spiral-shaped bacterial cells

Spirilla (singular: spirillum)

Morphological term for flexible and undulating spiral-shaped bacterial cells

Spirochetes

Morphological term for comma-shaped or curved rod bacteria

Vibrio

Diplococci arrangement definition and examples

Pairs of spherical bacterial cells formed based on their plane of division; examples include Streptococcus pneumoniae and Neisseria gonorrhoeae.

Streptococci arrangement definition and example

Bacterial cells arranged in chains; an example is Streptococcus pyogenes.

Staphylococci arrangement definition and example

Spherical bacterial cells arranged in grape-like clusters; an example is Staphylococcus aureus.

Etymological origin of the specific name aureus in Staphylococcus aureus

Derived from the Latin word for gold, referring to the golden color of its colonies on solid media.

Chemical charge and mechanism of basic dyes in staining

Positively charged molecules (cations) that enter and bind to negatively charged bacterial cell surfaces in positive staining.

Chemical charge and mechanism of acidic dyes in staining

Negatively charged molecules (anions) that are repelled by negatively charged cell surfaces, coloring the background in negative staining.

Examples of dyes commonly used in simple staining

Methylene blue, safranin, carbol fuchsin, and crystal violet

Definition and purpose of a mordant in differential staining

A substance (such as Gram's iodine) that sets a dye inside a cell and makes the coloring permanent by forming an insoluble complex.

Sequential steps of the Gram stain procedure

1. Apply crystal violet primary stain ($1\,\text{min}$)
2. Add Gram's iodine mordant ($1\,\text{min}$)
3. Decolorize with alcohol wash (short rinse)
4. Apply safranin counterstain ($1\,\text{min}$)

Color outcomes of Gram-positive and Gram-negative bacteria in Gram staining

Gram-positive cells appear purple (retain crystal violet); Gram-negative cells appear pink or red (counterstained with safranin).

Effect of cell age on Gram-positive staining results

Older Gram-positive cells develop leaky cell walls, causing them to lose crystal violet during the alcohol wash and falsely stain pink or red.

Dyes used in negative (capsule) staining and visual appearance of the capsule

Nigrosin or India ink; the capsule appears as a clear halo surrounding the bacterium against a dark stained background.

Key pathogenic functions provided by a bacterial capsule

Facilitates adherence to host tissues, protects against phagocytosis, and limits access of antibiotics, antiseptics, and disinfectants.

Diagnostic purpose and mechanism of flagella staining

Uses coats of dye or metals (such as silver) built up in layers to coat thin bacterial motility structures so they become visible under a light microscope.

Primary clinical pathogens identified using the Ziehl-Neelsen acid-fast stain

Mycobacterium tuberculosis (tuberculosis) and Mycobacterium leprae (leprosy).

Key cell wall component responsible for acid-fastness in Mycobacterium species

Mycolic acid (a waxy lipid molecule)

Reagents and order of application in Ziehl-Neelsen acid-fast staining

1. Primary stain with heated carbol fuchsin
2. Decolorization with acid-alcohol solution
3. Counterstaining with methylene blue

Staining results for acid-fast positive versus acid-fast negative bacteria

Acid-fast positive cells appear vivid red (retain carbol fuchsin); non-acid-fast cells appear blue (counterstained with methylene blue).

Steps and staining results of the endospore stain

1. Heat sample with malachite green for $5\,\text{min}$

2. Wash with water for $30\,\text{s}$

3. Counterstain with safranin Results: Endospores appear green, while non-spore cell bodies appear red.

Historical impact of the 14th-century Black Death (bubonic plague) on host genetic selection

Killed $33\%$ to $50\%$ of Europe's population; individuals with blood type B were more susceptible and had higher mortality rates.

Mutualistic microorganisms

Organisms that rely on the host for survival while providing benefits such as vitamin production, food digestion, and defense against pathogens.

Opportunistic pathogens

Microorganisms that cause disease only when presented with an opportunity, such as a host's compromised defenses or increased susceptibility.

Primary (obligate) pathogens

Organisms with specialized mechanisms that allow them to overcome intact host defenses and cause disease in healthy individuals.

Two fundamental requirements for any pathogen to establish infection and maintain survival

1. Multiplying in sufficient numbers to establish in the host
2. Transmissibility to new hosts

Pathogenic role of host symptoms like coughing and diarrhea

They promote transmission of the pathogen to new hosts (coughing spreads respiratory pathogens; diarrhea spreads gastrointestinal pathogens).

Evolutionary comparison of transmission efficiency between HIV and Marburg virus

HIV progresses slowly, allowing host survival for prolonged transmission; Marburg virus kills hosts rapidly, causing outbreaks to die out quickly.

Subclinical resolution of an infection

An outcome where a pathogen causes host damage without producing overt clinical symptoms, allowing hidden transmission to continue.

Definition of virulence

A measure of a pathogen's fitness in fighting host defenses and the degree of harm it causes to the host.

Four essential steps in bacterial pathogenicity

1. Adhere to, penetrate, and persist in host cells ("get-in-and-stay-in")
2. Avoid, evade, or compromise host defenses
3. Damage the host and permit infection spread
4. Exit the host and infect another host

Pathogenicity islands

Specific clusters of virulence genes located on the bacterial chromosome that coordinate pathogenic functions.

Plasmids in bacterial virulence

Mobile extrachromosomal DNA elements that transfer virulence genes or antibiotic resistance between bacterial cells.

Quorum sensing

A population-density-dependent communication mechanism where bacteria release and detect diffusible signaling molecules to regulate gene expression (such as virulence factors).

Auto-induction in quorum sensing

The process where accumulated signaling molecules reach a threshold concentration, triggering transcription of specific target genes across the bacterial population.

Types of signaling molecules released in quorum sensing by Gram-negative vs. Gram-positive bacteria

Gram-negative: N-acyl homoserine lactones; Gram-positive: peptides.

Proportional difference in quorum sensing regulation between opportunistic and primary pathogens

Opportunistic pathogens (such as Pseudomonas aeruginosa) regulate $5\%$ to $20\%$ of virulence genes via quorum sensing; primary pathogens (such as Staphylococcus aureus) control all virulence genes via quorum sensing.

Medical challenges posed by bacterial biofilms

They impede penetration of antimicrobial agents and host defenses, adhere strongly to medical implants, and are difficult to clean or maintain.

Mechanism and outcome of frustrated phagocytosis in biofilms

Host phagocytes fail to engulf an adhering biofilm, forming giant dead cells and a collagen capsule that impedes new blood vessel development and wound healing.

Initial host response to an implanted medical device prior to bacterial biofilm formation

The body coats the device with a protein film composed of fibronectin, fibrinogen, albumin, immunoglobulins, and other proteins that act as bacterial binding sites.

Four potential steps or fates of bacteria within a biofilm on a medical device

1. Accumulate on the device surface
2. Detach into surrounding fluid
3. Resist host defenses
4. Detach as large fragments that spread infection or cause fatal thromboembolisms

Nuclear differences between prokaryotic and eukaryotic cells

Prokaryotes have genetic material in an unenclosed nuclear region (nucleoid) without histones; eukaryotes have paired chromosomes enclosed in a membrane-bound nucleus with histones and a nucleolus.

Ribosomal differences between prokaryotic and eukaryotic cells

Prokaryotes possess $70S$ ribosomes; eukaryotes possess $80S$ ribosomes in the cytoplasm/ER and $70S$ ribosomes inside mitochondria.

Structural lipid differences in plasma membranes of bacterial, human, and fungal cells

Bacterial plasma membranes lack sterols; human membranes contain cholesterol; fungal membranes contain ergosterol.

Cell wall structural components in bacteria versus fungi versus animals

Bacteria: peptidoglycan, lipopolysaccharide, teichoic acid; Fungi: chitin; Animals: no cell wall.

Comparison of cellular respiration (ATP synthesis) site in prokaryotes versus eukaryotes

Prokaryotes generate ATP at the cell membrane; eukaryotes generate ATP in mitochondria.

Fluid mosaic model of the plasma membrane

Describes the membrane as a flexible phospholipid bilayer with floating proteins and carbohydrates that move freely through the structure.

Host cell receptor utilized by rhinovirus for cellular attachment and entry

ICAM-1 receptor located on respiratory epithelial cells.

Viral envelope origin and function

An outer membrane acquired from the host plasma membrane as the virus exits, aiding in entry into new host cells and protection against host defenses.

Microfilaments composition and role in cellular infection

Solid fibers composed of actin; pathogens like Shigella species and Listeria monocytogenes propel themselves through host cell cytoplasm and into adjacent cells using host actin tails.

Intermediate filaments composition and cellular function

Cytoskeletal structures made of keratin subunits that provide structural stability and help position cells within tissues.

Microtubules composition and major roles

Hollow tubes composed of tubulin that move chromosomes during cell division and form structural frameworks for cilia and flagella.

Structural microtubule arrangement of eukaryotic cilia

A $9+2$ arrangement consisting of an outer ring of nine microtubule pairs encircling two central single microtubules.

Mucociliary escalator host defense mechanism

Ciliated cells in the lower respiratory tract beat synchronously to sweep trapped foreign particles and pathogen-laden mucus upward and out of the respiratory tract.

Pathogen that attaches to respiratory ciliated cells to cause whooping cough

Bordetella pertussis

Concept of selective toxicity in antibiotic therapy

The ability of an antimicrobial agent to specifically target and destroy bacterial structures (such as $70S$ bacterial ribosomes) without harming eukaryotic host structures (such as $80S$ ribosomes).

Endosymbiotic theory

An evolutionary theory proposing that eukaryotic mitochondria originated from primitive prokaryotes that were integrated into early eukaryotic host cells.

Evidence supporting the endosymbiotic origin of mitochondria

Mitochondria possess circular DNA, replicate independently, contain $70S$ ribosomes, and generate ATP on inner membrane cristae similarly to bacteria.

Functional difference between rough and smooth endoplasmic reticulum

Rough ER has attached ribosomes and synthesizes proteins; smooth ER lacks ribosomes and synthesizes lipids and non-protein compounds.

Three main functions of the Golgi apparatus

1. Modifying and packaging products from the ER

2. Renewing the plasma membrane

3. Producing lysosomes

Lysosome function and role in innate immunity

Golgi-derived, membrane-enclosed vesicles containing digestive enzymes that fuse with phagocytic vesicles to destroy engulfed pathogens and recycle old host organelles.

Proteasome function and role in immune recognition

Stacked ring organelles that degrade ubiquitin-tagged host and pathogen proteins into small peptide fragments, which are transferred to the ER and cell surface to trigger an immune response.

Peroxisome function and enzymatic breakdown of hydrogen peroxide

Organelles involved in fatty acid breakdown that contain the enzyme catalase to decompose toxic $H_2O_2$ into $O_2$ and $H_2O$.

Nucleolus location and primary function

A dense body located inside the nucleus responsible for synthesizing ribosomal RNA (rRNA).

Pinocytosis

A form of endocytosis where the plasma membrane indents to engulf surrounding extracellular fluid and small dissolved molecules into a vesicle.

Phagocytosis

An endocytic process where pseudopodia extend outward to surround and engulf large particles or invading pathogens into a membrane-bound vesicle.

Receptor-mediated endocytosis

A selective form of endocytosis where specific target molecules bind to cell surface receptors, triggering membrane invagination and vesicle formation.

Exocytosis

The cellular process in which internal membrane-bound vesicles (from the ER or Golgi) fuse with the plasma membrane to release their contents outside the cell.