Lecture 10: Viruses and Bacteriophage Replication

Flashcards reviewing viral structure, replication cycles, Baltimore classification, genome replication strategies, and bacterial host defense systems.

What is an obligate intracellular parasite?

A biological genetic element, such as a virus, that can multiply only inside a living host cell because it requires the host cell for energy, metabolic intermediates, and protein synthesis.

What is a virion?

The complete extracellular form of a virus that exists outside the host cell and facilitates transmission from one host cell to another.

How do viruses differ from typical bacteria regarding nucleic acids, plasma membranes, and ribosomes?

Viruses possess either DNA or RNA (never both), lack a plasma membrane, and lack ribosomes, whereas typical bacteria possess both DNA and RNA, have a plasma membrane, and contain ribosomes.

What structural features are present in all viruses versus only some viruses?

All viruses possess a nucleic acid genome and a protein shell called a capsid. Only some viruses possess an outer lipid envelope.

What is the distinction between a capsid, a capsomere, and a nucleocapsid?

A capsid is the overall protein shell, a capsomere is an individual protein subunit of the capsid, and a nucleocapsid refers to the combined nucleic acid and protein shell of enveloped viruses.

What are the three primary morphological categories of viral capsid structures?

Helical, polyhedral, and complex.

Identify the labeled structural features of the T-even bacteriophage shown in the diagram.

The structure consists of an icosahedral capsid (head) containing DNA, connected to a sheath, tail fibers, a baseplate, and pins.

What occurs during the eclipse period of a viral growth curve?

The initial phase of infection in which viral genomes are uncoated inside host cells, resulting in no detectable extracellular virions.

How are bacteriophages quantified using the plaque assay method?

A mixture of phages and bacterial host cells in molten top agar is poured onto a nutrient agar plate; during incubation, phage infection and cell lysis produce clear zones called plaques within the bacterial lawn.

What are the five main steps in the lytic cycle of bacteriophage multiplication?

1. Attachment
2. Penetration
3. Biosynthesis
4. Maturation
5. Release

What is a prophage?

A viral genome that has integrated into the bacterial host chromosome during the lysogenic cycle and replicates along with the host cell during division.

What is phage conversion?

A phenomenon where a host bacterium acquires new phenotypic properties, such as toxin production in Vibrio cholerae or Corynebacterium diphtheriae, due to genes carried on an integrated prophage.

What are the two major entry pathways for animal viruses into host cells?

Receptor-mediated endocytosis and direct fusion of the viral envelope with the host plasma membrane.

What are the four primary outcomes of animal cell infection by viruses?

1. Virulent infection (host cell lysis)
2. Latent infection (viral DNA remains as provirus or episome without virion production)
3. Persistent infection (slow, continuous release of virions by budding without cell lysis)
4. Transformation (conversion of a normal cell into a tumor cell)

How do plant viruses spread from an infected cell to adjacent plant cells?

They enter through insect bites or wounds and move cell-to-cell through plasmodesmata using specialized movement proteins.

What makes Pandoravirus an exceptional eukaryotic virus?

It possesses an exceptionally large double-stranded DNA genome of $2.5\,\text{Mb}$ that infects amoebas, with approximately $93\%$ of its genes uncharacterized in any other organism.

According to the Baltimore classification scheme, how do Class IV and Class V ssRNA viruses differ in generating mRNA (+)?

Class IV ssRNA (+) genomes function directly as mRNA (+), whereas Class V ssRNA (-) genomes must undergo transcription of the minus strand by viral RNA dependent RNAP to produce mRNA (+).

How do Class VI retroviruses produce mRNA (+) from their ssRNA (+) genome?

They use reverse transcriptase to synthesize a double-stranded DNA intermediate, which integrates into the host genome and is transcribed by host RNA polymerase into mRNA (+).

What replication mechanism is utilized by single-stranded DNA bacteriophages such as $\Phi X174$?

Rolling circle replication, initiated when a viral gene product nicks the double-stranded replicative form intermediate to synthesize new single-stranded genome copies.

What is circular permutation and headful packaging in bacteriophage T4?

Genome replication forms concatemers that are cut into lengths filling each phage head ("headful"), resulting in genomes with identical gene content but different terminal sequence start points.

How do adenoviruses replicate their linear dsDNA genome without forming a lagging strand?

They use terminal proteins attached to the $5'$ ends of the DNA strands, enabling continuous leading-strand synthesis of both strands.

How does poliovirus process its viral proteins after translation?

Its (+)ssRNA genome is translated into a single large polyprotein, which is cleaved into individual functional proteins by viral proteases.

Why must negative-sense single-stranded RNA (Class V) viruses like rabies packaged an RNA replicase enzyme inside their virions?

Host cells lack an RNA-dependent RNA polymerase required to transcribe the negative-strand genomic RNA into positive-strand mRNA (+).

What two major envelope glycoproteins are present on influenza viruses?

Hemagglutinin and Neuraminidase.

How does triple reassortment in influenza viruses lead to new pandemic strains?

When intermediate hosts such as swine are infected simultaneously by human, avian, and swine influenza viruses, the eight segmented RNA genomes mix and re-assort into novel viral genotypes.

Why must reovirus dsRNA genome replication occur entirely within the viral capsid or core?

Double-stranded RNA in the cytoplasm acts as a trigger for host antiviral immune defenses, so transcription and replication are sequestered inside the protein core.

In a bacterial Restriction-Modification (R-M) system, how does a cell distinguish its own DNA from foreign phage DNA?

Host DNA is methylated at specific recognition sites by a methyltransferase (MTase), protecting it from cleavage by a restriction endonuclease (REase) that degrades unmethylated foreign phage DNA.

How do jumbo phages protect their genomes against host bacterial CRISPR-Cas and restriction enzyme systems?

They assemble a protein shell called a phage nucleus inside the host cell that encapsulates viral DNA and excludes host restriction enzymes and Cas nucleases.