Viruses, Viroids, Prions & Microbial Metabolism – Core Vocabulary

A comprehensive set of vocabulary flashcards covering viral structure, replication, taxonomy, prions, microbial metabolism, energy pathways, and key microbial groups to aid exam preparation.

Virus

Obligate intracellular parasite containing either DNA or RNA and a protein coat.

Virion

A complete, fully developed viral particle capable of infection.

Capsid

Protein coat surrounding viral nucleic acid; built from capsomeres.

Capsomere

Protein subunit that assembles to form a viral capsid.

Envelope (virus)

Lipid–protein–carbohydrate layer external to the capsid in some viruses.

Spikes

Surface projections on some enveloped viruses used for attachment.

Host range

Spectrum of host cells a virus can infect; determined by receptor compatibility.

Bacteriophage

Virus that infects bacteria.

Plaque

Clear zone on bacterial lawn where phage has lysed cells; quantified as PFU.

PFU (plaque-forming unit)

Measurement representing one infectious phage particle.

Baltimore classification

System grouping viruses into seven classes based on nucleic acid and mRNA strategy.

Helical virus

Virus with hollow, cylindrical capsid shaped like a helix (e.g., rabies, Ebola).

Polyhedral virus

Many-sided virus, often icosahedral (e.g., adenovirus).

Complex virus

Virus with complicated structures such as bacteriophage T4.

Lytic cycle

Phage replication process that ends with host cell lysis and release of virions.

Lysogenic cycle

Phage DNA integrates as a prophage and replicates without killing host.

Prophage

Phage genome integrated into bacterial chromosome during lysogeny.

Lambda phage

Temperate bacteriophage exhibiting lysogenic cycle in E. coli.

Attachment (virus)

First step of infection; virus binds specific host receptors.

Entry

Virus penetrates host cell via receptor-mediated endocytosis or fusion.

Uncoating

Separation of viral nucleic acid from its capsid inside the host cell.

Biosynthesis (viral)

Host machinery synthesizes viral nucleic acids and proteins.

Maturation (viral)

Assembly of viral components into complete virions.

Release (viral)

Exit of new virions by budding (enveloped) or lysis (non-enveloped).

• strand RNA

Single-stranded viral RNA that serves directly as mRNA.

– strand RNA

Single-stranded viral RNA complementary to mRNA; must be transcribed to + strand.

RNA-dependent RNA polymerase

Viral enzyme that replicates RNA genomes.

Reverse transcriptase

Enzyme that synthesizes DNA from an RNA template in retroviruses.

Retrovirus

RNA virus (e.g., HIV) that uses reverse transcriptase and forms a provirus.

Provirus

Viral DNA integrated into eukaryotic host genome, permanent like a gene.

Oncogenic virus

Virus capable of inducing tumors by integrating oncogenes into host DNA.

Oncogene

Mutated proto-oncogene that drives uncontrolled cell growth.

TSTA (tumor-specific transplantation antigen)

Surface antigen on virally transformed tumor cells.

Latent viral infection

Virus remains dormant in host, reactivates later (e.g., HSV, varicella).

Persistent viral infection

Chronic infection where virus is continuously produced over years.

Prion

Infectious protein particle lacking nucleic acid; causes spongiform encephalopathies.

PrP^C

Normal cellular prion protein.

PrP^Sc

Abnormal misfolded prion protein that aggregates and is infectious.

Adenoviridae

Non-enveloped dsDNA viruses causing respiratory infections.

Poxviridae

Large enveloped dsDNA viruses causing smallpox and MPOX.

Herpesviridae

Enveloped dsDNA viruses including HSV, VZV, EBV, CMV; exhibit latency.

Papillomavirus

Non-enveloped dsDNA virus; some types cause warts and cervical cancer.

Hepadnaviridae

Enveloped dsDNA viruses using reverse transcriptase; e.g., hepatitis B.

Coronaviridae

Enveloped +ssRNA viruses with crown-like spikes; includes SARS-CoV-2.

Togaviridae

Enveloped +ssRNA viruses; includes alphaviruses like EEE virus.

Rhabdoviridae

Enveloped –ssRNA bullet-shaped viruses; e.g., rabies virus.

Picornaviridae

Small non-enveloped +ssRNA viruses; includes poliovirus, rhinovirus, HAV.

Reoviridae

Non-enveloped dsRNA viruses; includes rotavirus.

PFV (filovirus)

Enveloped –ssRNA filamentous virus family (Ebola, Marburg).

Oncolytic virus

Engineered or natural virus that selectively infects and destroys cancer cells.

Metabolism

Sum of all chemical reactions in a cell, including catabolism and anabolism.

Catabolism

Exergonic breakdown of complex molecules, releasing energy and building blocks.

Anabolism

Endergonic synthesis of complex molecules from simpler ones using energy.

ATP (adenosine triphosphate)

Energy currency linking catabolic and anabolic reactions.

Enzyme

Biological catalyst that speeds reactions by lowering activation energy.

Active site

Region on enzyme where substrate binds.

Activation energy

Energy required to start a chemical reaction; lowered by enzymes.

Substrate

Reactant on which an enzyme acts.

Turnover number

Number of substrate molecules converted per enzyme per second.

Competitive inhibitor

Molecule that binds enzyme active site, blocking substrate.

Noncompetitive inhibitor

Binds allosteric site, altering active site shape and function.

Feedback inhibition

End-product inhibits earlier enzyme, controlling metabolic pathway.

Ribozyme

Catalytic RNA molecule that cuts and splices RNA.

Oxidation

Loss of electrons from a molecule.

Reduction

Gain of electrons by a molecule.

Redox reaction

Paired oxidation and reduction events.

Substrate-level phosphorylation

ATP formation by direct transfer of phosphate to ADP from a phosphorylated substrate.

Oxidative phosphorylation

ATP generation using electron transport chain and chemiosmosis.

Photophosphorylation

Light-driven ATP synthesis in photosynthetic cells.

Chemiosmosis

Use of proton gradient to drive ATP synthase.

Glycolysis

Oxidation of glucose to pyruvate yielding net 2 ATP and 2 NADH.

Pentose phosphate pathway

Alternate glucose oxidation producing NADPH and pentoses.

Entner–Doudoroff pathway

Glucose catabolism pathway producing NADPH, NADH, and ATP in some bacteria.

Transition step

Conversion of pyruvate to acetyl-CoA with CO₂ release and NADH production.

Krebs cycle

Series oxidizing acetyl-CoA to CO₂ while generating NADH, FADH₂, and ATP.

Electron transport chain (ETC)

Series of membrane carriers that pass electrons and pump protons.

Proton motive force

Electrochemical gradient of protons across a membrane driving ATP synthesis.

Aerobic respiration

Respiration using O₂ as final electron acceptor; maximum ATP yield.

Anaerobic respiration

Respiration using inorganic non-oxygen final acceptors (e.g., NO₃⁻, SO₄²⁻).

Fermentation

Anaerobic process using organic molecule as electron acceptor, producing little ATP.

Lactic acid fermentation

Conversion of pyruvate to lactic acid; regenerates NAD⁺.

Alcohol fermentation

Pyruvate converted to ethanol and CO₂; regenerates NAD⁺.

Photosynthesis

Light energy conversion to chemical energy followed by carbon fixation.

Calvin-Benson cycle

Light-independent pathway reducing CO₂ to glucose using ATP/NADPH.

Taxonomy

Science of classifying organisms into taxa based on similarities.

Systematics (phylogeny)

Study of evolutionary relationships among organisms.

Binomial nomenclature

Two-part scientific naming system of genus and species epithet.

Domain

Highest taxonomic rank; Bacteria, Archaea, Eukarya.

Endosymbiont theory

Hypothesis that mitochondria and chloroplasts evolved from engulfed bacteria.

Proteobacteria

Largest bacterial phylum of Gram-negative chemoheterotrophs (α, β, γ, δ, ε).

Firmicutes (Bacillota)

Low G+C Gram-positive bacteria including Bacillus, Clostridium, Staphylococcus.

Actinobacteria (Actinomycetota)

High G+C Gram-positive bacteria such as Mycobacterium and Streptomyces.

Extremophile

Archaeon thriving in extreme conditions (temperature, salinity, pH).

Halophile

Organism requiring high salt concentrations (>25%).

Thermophile

Organism growing optimally at ≥80 °C.

Methanogen

Anaerobic archaeon producing methane from CO₂ or acetate.

Endospore

Highly resistant dormant form produced by some Gram-positive bacteria.

Taq polymerase

Heat-stable DNA polymerase from Thermus aquaticus used in PCR.

Streptococcus pyogenes

β-hemolytic Group A streptococcus causing pharyngitis and scarlet fever.

Clostridioides difficile

Endospore-forming anaerobe causing antibiotic-associated colitis.