Chapter 6 Microbiology: Viruses, Phages, Viroids, and Prions

What is a virus?

A noncellular particle that is an obligatory intracellular parasite, infecting a host cell to produce progeny particles.

What is a virus particle or virion?

It consists of a viral genome (DNA or RNA) contained within a protein capsid, which may have appendages.

How do viruses infect host cells?

By insertion (bacteriophage) or by entry of the entire virus (most eukaryotic viruses).

What are bacteriophages?

Viruses that infect bacteria, such as bacteriophage P-SSP7 and T2.

What is a plaque in bacteriophage studies?

A clear spot of lysed cells on a lawn of bacteria, arising from a single virion.

What is the plaque count?

The number of individual infective virions from the phage suspension spread on a plate.

What is a prophage?

A bacteriophage that integrates its genome into the DNA of a bacterial genome.

What is a provirus?

An integrated viral genome within a human cell.

What is an endogenous virus?

A permanently integrated provirus transmitted from one human to another via the germ line.

What are the three forms a virus may interconvert among?

1. Virion/virus particle, 2. Intracellular replication complex, 3. Viral genome integrated within host DNA.

What is the structure of a virion?

It consists of nucleic acid enclosed by a protein capsid and may include enzymes and a lipid envelope.

What is the role of the intracellular replication complex?

It directs the host cell's enzymes to make and assemble progeny virions.

What is a virocell?

A virus-infected cell that produces viral proteins.

What is the argument regarding the living status of viruses?

Viruses are considered nonliving due to their inert nature, lack of metabolism, and inability to reproduce independently.

What is the genome of a virus?

It can either be DNA or RNA.

What is the function of the capsid in a virus?

It packages the viral genome and delivers it into the host cell, protecting it from degradation.

What is the envelope of some viruses?

A membrane derived from the previous host cell, incorporating glycoproteins that enable attachment and infection of the host cell.

What is the core particle of an enveloped virus?

The protein capsid of an enveloped virus.

What does the Tailed Virus structure include?

A protein capsid containing double-stranded DNA genome and a sheath with tail fibers for attachment.

What are viroids?

Infectious agents simpler than viruses that consist of a circular, ssRNA.

How do viroids avoid breakdown by host enzymes?

They double back on themselves to form base pairs interrupted by short, unpaired loops.

What is a prion?

An aberrant form of a normal protein arising from the host cell that has no nucleic acid component.

How do prions affect normal proteins?

They bind to normally folded proteins of the same class and alter their conformation.

What is the lytic cycle of bacteriophages?

A replication cycle where the phage immediately reproduces as many progeny phage particles as possible after genome entry.

What happens during the lytic cycle's burst phase?

The host cell wall is lysed, releasing mature virions.

What is lysogeny in bacteriophages?

A process where a temperate phage integrates its genome as a prophage into the host DNA.

What is transduction in bacteriophages?

The process of transferring host genes from one bacterium to another.

What is the slow-release replication cycle in bacteriophages?

A cycle where phage particles reproduce without destroying the host cell.

What are the three types of bacteriophage replication cycles?

Lytic cycle, lysogeny, and slow-release replication.

What factors determine which bacteriophage cycle will be followed?

The condition of the host and environmental stress.

What are some bacterial defenses against bacteriophage infection?

Genetic resistance, restriction endonucleases, and CRISPR.

What is CRISPR?

A bacterial immune system involving short DNA sequences.

What are gut bacteriophages?

Bacteriophages that are part of the mammalian intestinal community, modulating human digestion, immune system, and mental health.

What is the role of bacteriophages in the gut?

They are part of a microbial community that modulates human digestion and immune system.

How do host bacteria evolve resistance to phage attachment?

By mutating the amino acid sequences of their surface receptors.

What components do phages bind to in Salmonella?

LPS components, membrane proteins, and flagellar proteins.

What is the function of early genes in the lytic cycle?

They are expressed first to synthesize viral proteins.

What enzyme is expressed by late genes in the lytic cycle?

An enzyme that lyses the host cell wall.

What is the burst size in the lytic cycle?

The number of virus particles released after lysis.

How do filamentous phages reproduce?

They extrude through the cell envelope, allowing host cells to grow slowly without dying.

What is the significance of the gut virome?

It plays a role in human digestion, immune response, and mental health.

What is the structure of viroids?

They consist of a circular, single-stranded RNA.

What is the primary method by which viroids infect plants?

Through a damaged cell wall.

What is the consequence of prion-induced cell death in the brain?

It leads to tissue deterioration and dementia.

What are gut bacteriophages (coliphages)?

Phages residing within the mammalian intestinal microbiome that infect resident gut bacteria such as *E. coli*.

What functional role does TolC play in bacterial cells?

It acts as an outer membrane transport/efflux channel protein involved in exporting molecules out of the cell.

Do viroids encode proteins? How do they replicate?

No, viroids do not encode any proteins. They rely entirely on host cell RNA polymerase enzymes for replication.

What structural feature characterizes tailed bacteriophages like T4?

An icosahedral head containing dsDNA attached to a contractile helical sheath, baseplate, and tail fibers.

What are the sequential steps of the lytic replication cycle in bacteriophages?

1. Host recognition and attachment 2. Genome entry 3. Viral gene expression and capsid assembly 4. Host cell lysis and virion release.

What is the chemical composition and primary function of viral spike proteins?

They are glycoproteins that bind specific surface receptors on host cells to enable viral attachment and entry.

In a plaque assay, what theoretical assumption is made regarding each individual plaque?

Each plaque arises from infection by a single infectious virus particle (virion) in the original sample.

What is a temperate bacteriophage?

A phage capable of either undergoing a lytic replication cycle or integrating its genome into the host chromosome to establish lysogeny.

How do bacterial restriction endonucleases selectively cleave incoming viral DNA?

They recognize and cleave unmethylated foreign viral DNA, whereas host bacterial DNA is protected by site-specific methylation.

What is viral transduction?

The process by which a bacteriophage accidentally packages host bacterial genes during prophage excision and transfers them to a new host bacterial cell.

What are the red external projections on an enveloped virus called?

Spike proteins (glycoproteins embedded in the membrane envelope that mediate host receptor binding).

Which kingdom of organisms is primarily infected by viroids?

Plants (e.g., citrus trees, potatoes, tobacco, tomatoes).

What molecular structural difference causes a normal host protein to become a disease-causing prion?

A change in protein folding/tertiary structure from a normal conformation to an abnormal conformation rich in beta-sheets.

Why do some lytic phages digest host DNA upon entering the cell?

To redirect cell resources toward viral production and prevent host gene expression.

What is a virion?

An inert extracellular virus particle consisting of nucleic acid enclosed within a protective protein capsid.

Which human protein provided by HERV-E aids liver lipid metabolism?

Apolipoprotein C1.

What is the function of 'late genes' expressed near the end of the lytic cycle?

They encode capsid structural proteins and lytic enzymes (e.g., endolysin) that degrade the host cell wall to release mature progeny.

What human endogenous retrovirus gene product plays a critical role in human placental development?

Syncytin-1 (a retroviral envelope protein encoded by HERV-W that mediates placental cell fusion).

How does viral structure determine host range and specificity?

Viral surface proteins (capsid proteins or envelope spikes) must precisely match and bind specific surface receptor molecules on the target host cell.

How do viral genomes differ from cellular organism genomes regarding nucleic acid types?

Viral genomes can consist of either DNA or RNA (never both), and may be single-stranded (ss) or double-stranded (ds).

If a plaque assay produces 30 clear plaques from a 0.1 mL plated volume of a 10^-5 phage dilution, how many PFU are estimated in the original sample?

3.0 x 10^7 PFU/mL.

What role does transduction play in bacterial evolution?

It drives horizontal gene transfer, allowing bacteria to acquire new genetic traits such as antibiotic resistance or toxin production.

Why is RNA generally less chemically stable than DNA inside cells?

Because the 2'-hydroxyl (2'-OH) group on ribose makes RNA prone to hydrolysis, and intracellular RNase enzymes degrade unpaired RNA rapidly.

What causes the characteristic skin rash in a child infected with measles virus?

An immune system reaction (inflammatory response) as host immune cells fight viral infection.

What two essential components must be present in every virion?

1. Viral genome (nucleic acid) 2. Protein capsid.

What mechanism allows some gut phages to cross the intestinal mucosal barrier?

Transcytosis across intestinal epithelial cells.

What is a bacteriophage (phage)?

A virus that specifically infects bacterial cells.

What host conditions favor maintaining lysogeny over entering the lytic cycle?

Strong, healthy host cell growth and favorable environmental conditions.

What triggers a prophage to excise from the host chromosome?

Environmental stress (such as UV radiation, chemical damage, or nutrient starvation) that threatens host cell survival.

How can lysogenic conversion benefit a host bacterial cell?

By providing beneficial prophage-encoded genes that express novel traits, such as virulence factors, toxins, or metabolic enzymes.

What is the primary function of the viral capsid?

To protect the enclosed viral genome from environmental degradation and facilitate delivery of the genome into an appropriate host cell.

What is the function of 'early genes' expressed during the lytic cycle?

They encode viral proteins needed for viral DNA replication, host gene takeover, and destruction of host genomic DNA.

Which model bacteriophage performs the slow-release replication cycle?

Filamentous phage M13.

How do progeny filamentous M13 phages exit the host bacterial cell?

They assemble at the cell membrane and extrude through export pores (such as P4 channels) in the cell envelope.

How does viroid single-stranded RNA protect itself from host RNase degradation?

It doubles back on itself through intramolecular base pairing to form pseudo-double-stranded regions interrupted by short unpaired loops.

What enzyme mediates the integration of a temperate phage genome into a bacterial chromosome?

A recombinase enzyme (mediating site-specific recombination between phage and host DNA).

What clinical outcomes result from prion accumulation in brain tissue?

Prion-induced neuronal cell death leads to brain tissue deterioration (spongiform encephalopathy) and dementia.

What is a viral plaque in a bacteriophage culture assay?

A clear zone on a lawn of bacteria growing on agar, created where phage infection has lysed bacterial cells.

Name a classic example of a plant virus that causes leaf discoloration and stunted growth.

Tobacco Mosaic Virus (TMV).

What is the Tobacco Mosaic Virus (TMV)?

A plant virus that infects tobacco and other plants.

How does the bacterial CRISPR-Cas system function as an adaptive immune system against phages?

It integrates short fragments of former viral DNA into its locus, transcribes guide RNAs, and uses Cas proteins to target and cleave matching viral DNA upon re-exposure.

What primary argument supports classifying viruses as non-living?

Virions are inert particles outside host cells that lack metabolism, energy conversion, and independent reproduction.

How is plaque count used to quantify infectious virions in a sample?

By counting the number of plaques (clear zones) on a plate and performing back-calculation based on sample dilution and volume added.

What is the primary mode of transmission for animal viruses like measles virus exiting host cells?

Budding through the plasma membrane, acquiring a lipid envelope containing host membrane lipid bi-layer and viral spike proteins.

What is a viral envelope, and from where is it derived?

A membrane layer surrounding the capsid in some viruses, derived from the host cell membrane during viral exit (e.g., budding).

How do abnormal prion proteins cause pathogenesis within a host cell?

They bind to normally folded proteins of the same class, induce them to refold into the abnormal conformation, and form insoluble aggregates leading to cell death.

How can host bacteria evolve genetic resistance against bacteriophage attachment?

By mutating the genes encoding their cell-surface receptor proteins to alter amino acid sequences, preventing phage binding.

What term designates an integrated viral genome within a human or eukaryotic host cell?

Provirus.

Compare virions, viroids, and prions based on genetic material and protein components.

Virion: Nucleic acid (DNA or RNA) + Protein capsid;

Viroid: Infectious ssRNA only (no protein);

Prion: Misfolded protein only (no nucleic acid).

How can gut phages shape the bacterial composition of the intestinal microbiome?

By selectively lysing specific bacterial strains, phages alter bacterial population distributions and permit competing beneficial species to flourish.

What is the term for the protein capsid when enclosed within a lipid envelope?

Core particle (or nucleocapsid).

List three human physiological functions modulated by the gut bacteriophage community.

1. Human digestion; 2. Immune system regulation; 3. Mental health / gut-brain axis communication.

What does the acronym CRISPR stand for in microbiology?

Clustered Regularly Interspaced Short Palindromic Repeats.

What replicative intermediate is formed after single-stranded DNA (+ssDNA) of phage M13 enters a host cell?

A double-stranded DNA (dsDNA) circular intermediate.

Identify three distinct surface structures on Gram-negative bacteria that serve as bacteriophage receptors.

1. Lipopolysaccharide (LPS) components; 2. Outer membrane transport proteins (e.g., OmpF, TolC); 3. Flagellar proteins.

How is a prophage replicated and passed on during lysogeny?

The host bacterium replicates the integrated viral prophage along with its own chromosome during cell division, passing it to both daughter cells.