Classification, Molecular Structure, and Reproduction of Viruses

Vocabulary flashcards covering the classification, molecular mechanisms, genetic regulation, and life cycles of DNA, RNA, and retrotranscribing viruses based on Prescott Microbiology Chapter 25.

International Committee on Taxonomy of Viruses (ICTV)

The authoritative body that classifies viruses based on virion characteristics including nucleic acid type, presence or absence of an envelope, capsid symmetry, and the dimensions of the virion and capsid.

Realm (in Viral Taxonomy)

The highest taxonomic rank for viruses, equivalent to domain in cellular organisms; examples include Duplodnaviria (dsDNA viruses), Monodnaviria (ssDNA viruses), and Riboviria (RNA viruses).

Baltimore System of Classification

A virus classification system that focuses on the viral genome structure and the specific pathway used to synthesize viral mRNA, categorizing viruses into basic replication and expression groups.

Temperate Bacteriophage

A bacteriophage, such as Escherichia virus lambda ($\lambda$), that is capable of either entering a productive lytic cycle to lyse the host cell or establishing lysogeny by integrating its genome as a prophage.

Cohesive Ends (cos Sites)

Single-stranded, complementary 12-nucleotide overhangs at the ends of the linear bacteriophage lambda ($\lambda$) dsDNA genome that base-pair to form an open circle upon injection into the host cytoplasm.

cI Protein ($\lambda$ Repressor)

The regulatory master repressor in bacteriophage lambda that binds to operators $O_L$ and $O_R$, represses transcription of all phage genes except its own, and binds the $P_{RM}$ promoter to activate its own transcription and maintain lysogeny.

cII Protein

A viral activator protein in bacteriophage lambda that plays a pivotal role in deciding between lysogeny and lysis; high early levels activate transcription of $int$ (integrase) and $cI$, promoting lysogeny.

Cro Protein

A regulatory protein in bacteriophage lambda that promotes the lytic pathway by repressing transcription of $cIII$ and $cI$, while activating its own transcription and that of the late regulatory protein $Q$.

RecA Protein (in $\lambda$ Induction)

A host bacterial SOS-response protein activated by DNA damage (such as from UV light) that interacts with the lambda repressor ($cI$), stimulating it to cleave itself and trigger excision and the lytic cycle.

Excisionase (xis Gene Product)

An enzyme induced during bacteriophage lambda induction that binds to integrase and reverses the integration process, excising the prophage DNA from the host chromosome.

Viral Tegument

A proteinaceous layer situated between the envelope and the icosahedral nucleocapsid characteristic of herpesvirus virions.

Productive Infection (Herpesviruses)

An explosive viral replication cycle where $50,000\text{ to }200,000$ virions are produced per host cell, resulting in host cell death due to degradation of host DNA.

Latent Infection (Herpesviruses)

A dormant infection occurring in neuronal cells where infectious virions cannot be detected, but the viral genome persists and can subsequently reactivate to initiate recurrent productive infections.

Nucleo-Cytoplasmic Large DNA (NCLD) Viruses

Also called megaviruses; large dsDNA viruses with genomes of $500\text{ to }2,500\,\text{kb}$ visible by light microscopy that are taken up by phagocytosis without specific receptor pairing and encode many replication enzymes.

Replicative Form (RF)

The double-stranded circular DNA intermediate synthesized from an infecting single-stranded circular plus-strand DNA genome by bacterial DNA polymerase (e.g., in bacteriophage $\phi\text{X174}$) to direct rolling-circle replication.

RNA-Dependent RNA Polymerase (RdRp)

A viral enzyme exhibiting both transcriptase activity (synthesizing viral mRNA from an RNA template) and replicase activity (synthesizing plus-strand RNA from minus-strand RNA and vice versa).

Rotavirus Virion

A non-enveloped, wheel-like dsRNA virion with three concentric capsid layers (outer VP7/VP4 spikes, middle VP6, inner VP2) containing an 11-segment dsRNA genome complexed with VP1 and VP3.

Positive-Strand RNA (+RNA) Viruses

Viruses whose RNA genome can act directly as mRNA upon entry into the host cell; the first protein translated is RNA-dependent RNA polymerase, which then copies the $+\text{RNA}$ into a $-\text{RNA}$ intermediate.

NSP14 Protein

A coronavirus nonstructural protein that exhibits proofreading exonuclease activity on viral RNA, supporting the accurate replication of large RNA genomes ($\sim 30,000\,\text{base pairs}$).

Ribosomal Frame Shifting

A translational mechanism where a ribosome pauses at an RNA secondary structure, causing the tRNA to slip back by $1\,\text{nucleotide}$ to continue translating in an alternate reading frame (e.g., joining ORF1a to ORF1b in SARS-CoV-2).

Subgenomic RNAs (sgRNA)

A set of nested, shorter positive-sense RNA transcripts produced in coronaviruses that share a common $5'$ leader and polyadenylated $3'$ end, utilized for translating viral structural and accessory proteins.

Negative-Strand RNA (-RNA) Viruses

Viruses whose genomes cannot function directly as mRNA; they must package a preformed RNA-dependent RNA polymerase within the virion to synthesize $+\text{mRNA}$ using the minus strand as a template.

Influenza Virus Structure

An enveloped Orthomyxovirus possessing 7 to 8 segmented linear negative-sense RNA nucleocapsids surrounded by an envelope studded with Hemagglutinin, Neuraminidase, and M2 ion channel proteins.

Antigenic Shift via Segment Reassortment

The generation of novel influenza strains with pandemic potential occurring when two different strains coinfect the same host cell and exchange entire RNA genome segments during virion assembly.

Reverse Transcriptase (RT)

A multifunctional, error-prone retroviral enzyme possessing RNA-dependent DNA polymerase, DNA-dependent DNA polymerase, and ribonuclease H activities to convert $+\text{ssRNA}$ into $+\text{dsDNA}$.

Ribonuclease H (RNase H)

An enzymatic activity of reverse transcriptase responsible for degrading the original RNA strand from the intermediate RNA:DNA hybrid during reverse transcription.

HIV-1 Virion

An enveloped retrovirus with a cone-shaped capsid enclosing two identical $+\text{ssRNA}$ genome molecules, reverse transcriptase, integrase, and protease, with surface gp120 docking glycoproteins and gp41 transmembrane proteins.

Provirus

The double-stranded viral DNA intermediate of a retrovirus (such as HIV) that has been permanently integrated into the host cell's nuclear chromosome by viral integrase.

Hepatitis B Virus Genome

A $3.2\,\text{kb}$ circular DNA molecule consisting of one complete nicked strand and a complementary strand with a large gap, covalently attached to viral polymerase P.