Microbiology: Virology, Acellular Entities, and Microbial Metabolism

Comprehensive practice flashcards reviewing virology, acellular agents, influenza epidemiology, and microbial metabolism based on lecture material.

Artificial Intelligence in Medical Education (Lazarus, 2026)

The technological inflection point where Large Language Models (LLMs) can pass licensing-style exams, draft clinical notes, simulate patients, and tutor trainees, but if improperly governed, threaten to corrode how physicians learn to think.

Pandoravirus massiliensis

A giant virus demonstrated by Aherfi et al. (2021) to possess a membrane potential and an incomplete tricarboxylic acid cycle with a proton gradient, challenging the conventional boundary between viruses and living organisms.

Virion

The extracellular, biologically inert structural state of a virus existing outside of the host cell, typically comprising a nucleic acid genome enclosed within a protein capsid.

Capsid

The outer protective shell of a virion, constructed of symmetrically arranged protein molecules (capsomers) that encases and protects the viral genome.

Viral Envelope

A host-derived phospholipid bilayer membrane embedded with virus-encoded spike proteins that surrounds the nucleocapsid of certain viruses.

Naked Virus

A non-enveloped virus that consists exclusively of a nucleocapsid without any surrounding lipid membrane.

Viral Budding

The exit mechanism employed by enveloped viruses wherein the viral nucleocapsid binds to viral envelope proteins aggregated in a host membrane (cell membrane, ER, or nuclear envelope) and extrudes outward, acquiring its lipid envelope without immediately lysing the cell.

Circovirus SFBeef

A single-stranded DNA (ssDNA mini-PCV) virus that has one of the smallest known viral genomes, measuring approximately $0.859\text{ kbp}$.

Pandoravirus salinus

A giant double-stranded DNA (dsDNA) virus possessing one of the largest recorded viral genomes, measuring approximately $2473\text{ kbp}$.

Hepatitis D Virus Genome

A human subviral satellite agent possessing an extremely compact RNA genome of approximately $1.8\text{ kb}$.

SARS-CoV-2 Genome

A positive-sense single-stranded RNA genome of approximately $30{,}000$ RNA letters encoding 29 proteins, structured with ORF1a and ORF1b followed by genes for the Spike (S), Envelope (E), Membrane (M), and Nucleocapsid (N) proteins.

Structural Viral Proteins

Viral proteins that constitute the physical architecture of the mature virion particle, such as capsid capsomers, envelope glycoproteins, and core proteins.

Non-structural Viral Proteins

Proteins produced inside the infected host cell that do not form part of the assembled virion, such as viral enzymes needed for genome replication and transcription.

Regulatory Viral Proteins

Proteins whose primary function is to govern the timing, progression, and expression levels of viral and host genes during the viral replication cycle.

Accessory Viral Proteins

Viral proteins that are non-essential for viral replication in cell culture, but play significant roles in pathogenesis, viral proliferation, or immune modulation in vivo.

Helical (Tubular) Capsid

A cylindrical or rod-shaped viral capsid architecture formed by protein subunits arranged in a spiral around a central nucleic acid core, exemplified by Tobacco Mosaic Virus (TMV) and Ebola virus.

Icosahedral Capsid

A symmetrical viral capsid architecture resembling a polyhedron with 20 equilateral triangular faces and 12 vertices, packaging nucleic acid tightly inside.

Binal Symmetry

A complex twofold capsid morphology characteristic of bacteriophages (such as T4 and $\lambda$), featuring an icosahedral head joined to a helical tail.

Bacteriophage T4 Baseplate

The multi-protein structure located at the distal tip of the contractile tail of phage T4 that anchors tail pins and fibers to execute final attachment and trigger sheath contraction.

Bacteriophage T4 Long Tail Fiber

A segmented sensory appendage composed of proteins gp34, gp35, gp36, gp37, and gp38 with a knee hinge and needle tip that mediates initial reversible attachment to the bacterial host cell surface.

OmpC

A bacterial outer membrane porin protein that, together with lipopolysaccharide (LPS), serves as the specific host-cell receptor recognized by bacteriophage T4.

Bacteriophage Penetration Mechanism

An ATP-independent entry process wherein initial attachment by tail fibers is followed by baseplate anchoring, tail sheath contraction, and mechanical driving of the rigid inner tube through the outer membrane, murein layer, and cell membrane to inject DNA into the cytoplasm.

Bacteriophage Ghost

An empty phage capsid that remains bound to the exterior surface of a bacterial host cell after injecting its viral DNA into the host cytoplasm.

Animal Virus Penetration by Membrane Fusion

An entry mechanism where the viral lipid envelope fuses directly with the host plasma membrane (or an endosomal membrane following receptor-mediated endocytosis), releasing the naked nucleocapsid into the host cytoplasm for uncoating.

Plasmodesmata

Microscopic cytoplasmic channels traversing plant cell walls through which plant viruses spread from cell to cell within infected plant tissues.

Cytoplasmic Replication of Poxviruses

An exception to the general rule that eukaryotic DNA viruses replicate in the nucleus; poxviruses are dsDNA viruses that carry out their entire replication cycle inside the cytoplasm.

Rolling Circle Replication

A mechanism of nucleic acid synthesis wherein an endonuclease nicks one strand of a circular dsDNA molecule to provide a free $3'\text{-OH}$ primer, allowing continuous synthesis along the intact strand while displacing a growing single-stranded tail that is copied into a long linear concatemer.

Positive-Sense Single-Stranded RNA ((+)ssRNA)

A viral RNA genome that possesses the same polarity as mRNA, allowing it to bind directly to host ribosomes upon entry and translate proteins, such as viral RNA-dependent RNA polymerase.

Negative-Sense Single-Stranded RNA ((-)ssRNA)

A viral RNA genome complementary to mRNA that cannot be translated directly by host ribosomes; the virion must package and deliver an active RNA-dependent RNA polymerase to synthesize positive-sense mRNA templates.

RNA-Dependent RNA Polymerase (RNA Replicase)

An enzyme encoded by RNA viruses that synthesizes a complementary RNA strand using an RNA template, a biochemical activity absent from uninfected host cells.

Norovirus (Norwalk Virus)

A non-enveloped, (+)ssRNA virus with a genome of approximately $7.3\text{--}7.5\text{ kb}$ and an extremely low infectious dose ($\text{ID}_{50} \approx 18\text{ particles}$) transmitted via the fecal-oral route or aerosolized vomitus.

Histo-Blood Group Antigens (HBGAs)

Complex carbohydrates expressed on mucosal epithelial cells in the human gastrointestinal tract that act as primary attachment receptors for different strains of Norovirus.

Rotavirus

A double-stranded RNA (dsRNA) virus responsible for approximately 50% of hospital visits for severe diarrhea in infants, historically causing between 80,000 and 500,000 global deaths annually (estimated at 151,000 in 2019).

Bluetongue Virus

A double-stranded RNA virus infecting ruminants that produces mortality rates ranging from 2% to 90%.

Pseudomonas Virus phi6

An enveloped bacteriophage infecting the plant pathogen Pseudomonas syringae that features a 3-part segmented double-stranded RNA genome.

Reverse Transcriptase

A multifunctional viral polymerase that reverse-transcribes single-stranded viral RNA into single-stranded DNA, degrades the original RNA strand, and synthesizes a complementary second DNA strand to generate double-stranded DNA.

Integrase

A retroviral enzyme carried inside the virion that inserts the blunt-ended dsDNA copy of the viral genome into a host cell chromosome to establish a provirus.

Provirus

A viral genome permanently integrated into the host eukaryotic chromosome, replicated passively whenever the host cell divides.

Parvovirus B19

A human single-stranded DNA (ssDNA) virus that causes Fifth Disease (erythema infectiosum or 'slapped cheek' disease); it is typically self-limiting but can cross the placenta, posing risks of miscarriage or stillbirth.

Canine Parvovirus

A highly contagious and severe ssDNA viral infection targeting the gastrointestinal tract of canines, frequently proving life-threatening.

Viral Polyprotein

A large precursor polypeptide translated from a polycistronic mRNA (often lacking internal stop codons) that is subsequently cleaved into individual functional viral proteins by a specific viral protease.

Headful Packaging Mechanism

A phage DNA packaging process wherein an empty capsid is stuffed with replicated viral concatemer DNA until physical internal capacity is reached, whereupon an endonuclease cleaves the genome to free the mature head.

Host Cell Lysis (Non-Enveloped Virions)

The standard release mechanism for non-enveloped bacteriophages and animal viruses, characterized by the catastrophic rupture of the host membrane and wall, releasing hundreds to thousands of progeny particles at once.

Hit and Run Viral Strategy

A viral lifestyle characterized by rapid replication, high virion shedding, acute clinical symptoms, and rapid immune clearance, exemplified by Influenza and Norovirus.

Slow and Low Viral Strategy

A viral infection tactic involving continuous, low-level shedding or prolonged quiescent periods over years without triggering severe host immune destruction, exemplified by Human Cytomegalovirus.

Latency with Occasional Reemergence

A viral survival tactic where the virus maintains an asymptomatic, dormant reservoir in host tissues (such as sensory neurons) punctuated by episodic reactivations and lytic shedding, exemplified by Herpes simplex viruses.

Bacteriophage Lambda (\lambda)

A temperate dsDNA bacteriophage infecting E. coli that attaches to the LamB outer membrane receptor and can choose between lytic destruction or lysogenic integration.

Temperate Phage

A bacteriophage capable of either executing a lytic replication cycle or establishing a stable, quiescent lysogenic relationship within its bacterial host.

Lysogeny

The non-lytic state in which a temperate phage genome is stably integrated into the host bacterial chromosome as a prophage and replicated synchronously with the host genome.

Prophage

The latent form of a bacteriophage genome integrated into the circular chromosome of a lysogenic bacterium.

Lysogen

A viable bacterial cell carrying a latent prophage integrated within its genome, rendering the bacterium immune to subsequent superinfection by the same phage type.

cI Repressor Protein

A phage $\lambda$ regulatory protein that binds to early viral operators to shut off transcription of lytic genes, thereby maintaining the lysogenic state.

Prophage Induction

The process by which an integrated prophage excises from the host bacterial chromosome and initiates the lytic cycle, typically triggered by host DNA damage or physiological stress.

Latency-Associated Transcripts (LATs)

Specific non-coding viral RNA molecules transcribed during latent herpesvirus infection that accumulate to maintain transcriptional silencing and promote episomal persistence in sensory neurons.

Herpesviridae

A family of enveloped linear dsDNA viruses (100–200 genes) that establish lifelong latency, including HSV-1 (orolabial), HSV-2 (genital), Varicella-zoster virus (chickenpox/shingles), and Epstein-Barr virus (mononucleosis and cancers).

Viroid

An infectious acellular plant pathogen consisting strictly of naked, non-coding, circular single-stranded RNA ($250\text{--}400\text{ nucleotides}$) that folds into a rod-like structure with extensive internal complementarity and replicates via a rolling circle mechanism.

Pospiviroidae

A family of plant viroids that localize and replicate inside the host cell nucleus.

Avsunviroidae

A family of plant viroids that replicate within chloroplasts and possess intrinsic ribozyme catalytic cleavage activity.

Prion (PrPSc)

An infectious, protein-only pathogen lacking nucleic acid that propagates by inducing a pathogenic conformational change in normal cellular prion proteins ($\text{PrP}^C$), converting predominant $\alpha$-helices into insoluble, protease-resistant $\beta$-pleated sheets.

Spongiform Encephalopathy Histopathology

The hallmark microscopic appearance of prion-diseased brain tissue, characterized by widespread neuronal vacuolation, severe astrogliosis, amyloid deposition, and spongiform changes.

Hemagglutinin (HA)

An influenza surface glycoprotein spike (18 known subtypes) that binds to sialic acid residues on host respiratory epithelial cells to mediate viral attachment and membrane fusion.

Neuraminidase (NA)

An influenza surface glycoprotein enzyme (11 known subtypes) that cleaves terminal sialic acid from host cell receptors and newly assembled virions to facilitate progeny release and prevent viral self-aggregation.

$\alpha(2,6)$ Sialic Acid Linkage

The specific chemical linkage between neuraminic (sialic) acid and galactose dominant on human upper respiratory tract epithelial cells, serving as the primary receptor for human-adapted influenza A viruses.

$\alpha(2,3)$ Sialic Acid Linkage

The chemical linkage between sialic acid and galactose found predominantly in the digestive tracts of waterfowl and respiratory tracts of chickens, preferentially bound by avian influenza strains.

Influenza Virus Nomenclature

The standardized naming convention for influenza isolates organized in the order: Virus Type / Geographic Place of Isolation / Strain Number / Year of Isolation (Subtype), such as A/Sydney/05/97 (H3N2).

Influenza Clades and Subclades

Monophyletic groups and subgroups on an influenza phylogenetic tree representing viruses whose hemagglutinin (HA) genes share common mutations inherited from a specific ancestral node.

Respiratory Droplet Transmission

The primary route of influenza transmission, occurring when an infected individual sneezes, coughs, or talks, expelling infectious moisture droplets that land directly on the mucosal membranes of nearby persons.

Influenza-Like Illness (ILI)

A public health surveillance case definition defined in Georgia and the CDC as fever (over $100^{\circ}\text{F}$ or $37.8^{\circ}\text{C}$) accompanied by a cough and/or a sore throat without a known alternate cause.

Live Attenuated Influenza Vaccine (LAIV3 / FluMist)

A needle-free intranasal spray vaccine containing live, cold-adapted, attenuated influenza viruses, approved for non-pregnant healthy individuals aged 2 through 49 years and manufactured using embryonated eggs.

Recombinant Influenza Vaccine (RIV3 / Flublok)

An egg-free influenza vaccine containing hemagglutinin antigens produced via recombinant baculovirus technology in insect cells, approved for individuals aged 9 years and older.

Cell-Based Influenza Vaccine (FLUCELVAX)

A standard-dose inactivated influenza vaccine grown in cultured Madin-Darby Canine Kidney (MDCK) cells rather than chicken eggs, approved for individuals aged 6 months and older.

Adjuvanted Inactivated Influenza Vaccine (FLUAD)

An egg-based inactivated trivalent vaccine approved for adults aged 65 years and older that contains squalene oil (MF59) as an adjuvant to heighten the immune response.

WHO Global Influenza Surveillance Network

An international surveillance consortium comprising five major reference centers (Atlanta, London, Melbourne, Tokyo, Beijing) that meets twice annually (February for the Northern Hemisphere, September for the Southern Hemisphere) to recommend annual vaccine strains.

VRBPAC 2026-2027 Egg-Based Formulation Recommendation

The FDA advisory committee recommendation formulated on March 12, 2026, comprising A/Missouri/11/2025 (H1N1)pdm09-like, A/Darwin/1454/2025 (H3N2)-like, and B/Tokyo/EIS13-175/2025 (B/Victoria lineage)-like viruses.

Baloxavir Marboxil (Xofluza)

A single-dose oral antiviral drug for influenza that selectively blocks viral transcription by inhibiting the cap-snatching endonuclease activity of the polymerase acidic (PA) protein.

Cap-Snatching

The transcription initiation mechanism of influenza virus wherein the viral PA endonuclease binds and cleaves the $5'$ methylated cap and adjacent 10–20 nucleotides from host cell pre-mRNAs to use as primers for viral mRNA synthesis.

Amantadine and Rimantadine

Adamantane antivirals that specifically inhibit the influenza A virus M2 proton channel to block viral uncoating; they are ineffective against influenza B and no longer recommended due to widespread resistance.

Epidemic Threshold (P&I Mortality)

The statistically calculated baseline curve representing the expected upper boundary of seasonal pneumonia and influenza deaths, above which an excess mortality surge indicates an active epidemic.

ILINet Surveillance System

The U.S. Outpatient Influenza-like Illness Surveillance Network that tracks weekly outpatient visits presenting with fever plus cough or sore throat relative to an established national baseline.

Chemotroph

An organism that obtains metabolic energy through the oxidation of preformed organic or inorganic chemical compounds rather than sunlight.

Phototroph

An organism that traps radiant light energy from the sun and converts it into chemical energy via photochemical reactions.

Autotroph

An organism that utilizes carbon dioxide ($\text{CO}_2$) as its sole or principal source of carbon for biosynthesis and cellular structure.

Heterotroph

An organism that requires preformed organic molecules as its primary source of cellular carbon.

Chemoorganoheterotroph

An organism that obtains metabolic energy from the oxidation of chemical compounds, derives electrons from organic donors, and assimilates organic carbon for biomass, encompassing most known bacteria, fungi, protozoa, and animals.

Chemoorganoautotroph

A rare metabolic type of organism that oxidizes organic chemical compounds to obtain energy and reducing equivalents while utilizing carbon dioxide ($\text{CO}_2$) as its primary carbon source, exemplified by anaerobic methanotrophic archaea and Pichia pastoris.

Chemolithoheterotroph

An organism that oxidizes inorganic compounds for energy and electron donor needs but requires organic carbon sources for cellular biosynthesis, exemplified by Oceanithermus profundus.

Chemolithoautotroph

An organism that extracts energy and electrons entirely from the oxidation of reduced inorganic minerals or chemicals and fixes carbon dioxide ($\text{CO}_2$) as its carbon source, exemplified by Nitrobacter.

Photoorganoheterotroph

An organism that absorbs sunlight for energy, uses organic compounds as electron/hydrogen donors, and assimilates organic molecules as its carbon source, exemplified by Rhodobacter, Heliobacterium, and purple non-sulfur bacteria.

Photoorganoautotroph

An organism that utilizes sunlight as an energy source and organic donors for electrons while fixing atmospheric carbon dioxide ($\text{CO}_2$), exemplified by certain Haloarchaea performing anoxygenic photosynthesis.

Photolithoheterotroph

An organism that harnesses light energy and utilizes inorganic compounds (such as reduced sulfur) as electron donors, yet depends on organic carbon for biomass.

Photolithoautotroph

An organism that utilizes light as its energy source, inorganic donors (such as $\text{H}_2\text{O}$ or $\text{H}_2\text{S}$) for electrons, and carbon dioxide ($\text{CO}_2$) for carbon, exemplified by cyanobacteria, eukaryotic algae, and land plants.

Anoxygenic Photosynthesis

A photosynthetic process that absorbs light energy to generate ATP without generating oxygen gas ($\text{O}_2$), utilizing electron donors other than water such as sulfide or organic molecules.

Fluid Thioglycollate Medium

A liquid reducing medium containing sodium thioglycollate that chemically scavenges dissolved oxygen, establishing an oxygen concentration gradient from fully aerobic at the top to strictly anoxic at the tube bottom.

Obligate Aerobe

An organism that strictly requires molecular oxygen ($\text{O}_2$) for respiration and growth, forming dense growth exclusively at the liquid-air interface of a thioglycollate tube (exemplified by Pseudomonas aeruginosa).

Obligate Anaerobe

An organism that lacks or possesses inadequate antioxidant protective enzymes against oxygen toxicity, growing only in anoxic zones at the bottom of thioglycollate broth (exemplified by Clostridium butyricum).

Facultative Anaerobe

An organism that can switch between aerobic respiration when oxygen is available and fermentation or anaerobic respiration when it is absent, growing throughout the depth of a thioglycollate tube with heaviest density at the top (exemplified by Escherichia coli and Staphylococcus aureus).

Microaerophile

An organism that requires oxygen for aerobic respiration but is inhibited by atmospheric concentrations (20%), growing in a narrow band slightly beneath the meniscus in thioglycollate medium (exemplified by Neisseria sicca).

Aerotolerant Anaerobe

An anaerobic organism with fermentative metabolism that does not use oxygen for respiration but tolerates oxygen exposure without toxicity, growing with uniform density throughout a thioglycollate tube.

Cellular Respiration

A catabolic process wherein an external electron donor is oxidized and electrons are passed through a membrane-bound electron transport chain to an external terminal electron acceptor, driving ATP synthesis predominantly via oxidative phosphorylation.

Fermentation

An anaerobic catabolic pathway in which an organic substrate acts as both the primary electron donor and terminal electron acceptor, producing ATP directly via substrate-level phosphorylation without an electron transport chain.