Chapter 6: Viruses and Bacteriophages: Structure, Life Cycles, and Host Interactions

What is a virus?

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

What is a virion?

A virus particle consisting of a viral genome (DNA or RNA) within a protein capsid.

How do viruses enter host cells?

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

What are bacteriophages?

Viruses that infect bacteria.

What is an example of a bacteriophage?

Bacteriophage P-SSP7 infects Prochlorococcus, and bacteriophage T2 infects E. coli.

What is a plaque in virology?

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 package enzymes and possess a lipid envelope.

What is a virocell?

A virus-infected cell that directs the cell's enzymes to make and assemble progeny virions.

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 are the components of a virus structure?

1. Genome (DNA or RNA), 2. Capsid (made of protein), 3. Envelope (if present, derived from the host cell's membrane).

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 role do glycoproteins play in viruses?

They enable the virus to attach to and infect the host cell.

What is the core particle of an enveloped virus?

The protein capsid of the virus.

What is the structure of the T4 bacteriophage?

It has a protein capsid containing double-stranded DNA, a sheath, and tail fibers for attachment to host cells.

What are viroids?

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

How do viroids avoid breakdown by host RNase 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 with no nucleic acid component.

How do prions cause disease?

They bind to normally folded proteins and alter their conformation, leading to harmful aggregates and cell death.

What is the lytic cycle of bacteriophages?

A replication cycle where phages immediately reproduce progeny after delivering their genome into a host cell.

What are the steps involved in the lytic replication cycle?

Host recognition and attachment, genome entry, assembly of phages, exit and transmission.

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 to other host cells during the exit from lysogeny.

What is the slow-release replication cycle in bacteriophages?

A cycle where phage particles reproduce without destroying the host cell, allowing the host to grow slowly.

What are the three forms of bacterial defenses against bacteriophage infection?

Genetic resistance, restriction endonucleases, and CRISPR.

What role do gut bacteriophages play in human health?

They modulate human digestion, immune system, and mental health.

What is the burst size in the lytic cycle?

The number of virus particles released after lysis of the host cell.

What happens during the lytic cycle after the phage genome enters the host cell?

Early genes are expressed to synthesize viral proteins, followed by late genes that lyse the host cell wall.

How can host bacteria evolve resistance to phage attachment?

By mutating the amino acid sequences of its surface receptors.

What is the difference between the lytic cycle and lysogeny?

Lytic cycle involves immediate multiplication of the virus, while lysogeny integrates the viral genome into the bacterial chromosome.

What is the function of restriction endonucleases in bacterial defenses?

They cleave viral DNA that lacks methylation.

What are CRISPR sequences?

Short DNA sequences that form part of a bacterial immune system.

What is the formal definition of a virus?

A noncellular particle and obligatory intracellular parasite that infects a host cell and directs it to produce progeny particles.

What is the inert, non-living form of a virus called?

Virion (or virus particle).

What two essential components are found in every virion?

A viral genome (DNA or RNA) and a protein capsid.

How do viruses of eukaryotes differ from bacteriophages in genome delivery?

Bacteriophages insert only their genome, whereas most eukaryotic viruses enter the host cell entirely.

What is the specific host of the bacteriophage $P-SSP7$?

The bacterium $Prochlorococcus$.

How is the replication of bacteriophages observed on a lawn of bacteria?

As plaques, which are clear spots of lysed cells on the Petri dish.

What is the theoretical origin of a single plaque on a bacterial lawn?

A single virion from the sample.

What is 'plaque count'?

The number of individual infective virions present in the original phage suspension.

What is the primary function of the viral capsid?

To package the viral genome, protect it from degradation, and deliver it into the host cell.

What is the term for the integrated genome of a bacteriophage within a bacterial host?

Prophage.

What is the term for an integrated viral genome in human cells?

Provirus.

What is an 'endogenous virus'?

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

What are the three interconvertible forms a virus may take during its life cycle?

1. Virion (virus particle) 2. Intracellular replication complex 3. Integrated viral genome.

What host machinery does a virus recruit to synthesize proteins in the intracellular replication complex?

Host ribosomes.

What is a 'virocell'?

A virus-infected cell that is actively producing virions.

What structural feature is found in animal viruses but absent in most bacteriophages?

An envelope.

What is the chemical composition of viral 'spikes'?

Glycoproteins (protein and carbohydrate complexes).

In an enveloped virus, what is the protein capsid referred to as?

Core particle.

What subviral agent consists solely of infective circular $ssRNA$ without a capsid?

Viroid.

How do viroids protect their $ssRNA$ from degradation?

By doubling back on themselves to form base pairs interrupted by short, unpaired loops.

In which kingdom of life do viroids primarily cause infections?

Plants.

What is a 'prion'?

An aberrant, infectious form of a normal host protein that lacks nucleic acids.

How do prions spread within a host?

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

What is the ultimate pathological result of prion aggregate accumulation in the brain?

Tissue deterioration and dementia (due to cell death).

To start an infection, what must bacteriophages bind to on the host cell?

Specific cell-surface receptors.

Name three types of host molecules in $Salmonella$ that bacteriophages co-opt as receptors.

1. $LPS$ (lipopolysaccharide) components 2. Membrane proteins ($OmpF$, $TolC$) 3. Flagellar proteins.

What is a phage 'ghost'?

The empty capsid that remains attached to the outside of the host cell after the genome has been injected.

What are the two primary types of replication cycles exhibited by bacteriophages?

The lytic cycle and lysogeny.

List the four main steps of the lytic replication cycle.

1. Host recognition and attachment 2. Genome entry 3. Assembly of phages 4. Exit and transmission.

Why do some phages like $T4$ digest the host DNA during the lytic cycle?

To increase the efficiency of phage production by repurposing host nucleotides.

What is 'burst size'?

The total number of virus particles released from a single lysed host cell.

Contrast 'early genes' and 'late genes' in the viral lytic cycle.

Early genes synthesize viral proteins for replication; late genes produce enzymes to lyse the host cell wall for exit.

What is a temperate phage?

A phage that can follow either a lytic or lysogenic path.

What mechanism integrates the phage genome into the host's DNA during lysogeny?

Site-specific recombination mediated by a recombinase enzyme.

What environmental factor can trigger a prophage to excise from the host genome?

Environmental stress (e.g., $UV$ light or chemicals that threaten host survival).

What is 'transduction'?

The process by which a virus acquires host genes during exit from lysogeny and transfers them to new host cells.

How does the 'slow-release' replication cycle differ from lysis?

Phage particles reproduce and extrude through the cell envelope without destroying the host cell.

Which specific phage is an example of the slow-release replication cycle?

Filamentous phage $M13$.

What serves as the template to synthesize the double-stranded intermediate in the M13 life cycle?

Circular ssDNA (single-stranded DNA).

What is the metabolic cost to a host cell undergoing slow-release viral replication?

The cell grows slowly because many of its resources are diverted to virus production.

Which viral gene in Phage C1 integrated into Clostridium botulinum is responsible for causing botulism?

The botulinum toxin gene (c1).

What human trait or protein is provided by the integrated endogenous retrovirus HERV-W?

Syncytin-1 (involved in placental fusion).

What toxin is produced by Vibrio cholerae that is encoded by a prophage gene?

Cholera toxin.

The toxin produced by Staphylococcus aureus causing toxic shock syndrome is carried by which prophage?

TSST-1.

Apart from genetic resistance, name two other bacterial defense mechanisms against phages.

Restriction endonucleases and CRISPR.

How do restriction endonucleases distinguish between host DNA and viral DNA?

They cleave DNA lacking specific methylation patterns (typically viral DNA).

What does the acronym CRISPR stand for?

Clustered Regularly Interspaced Short Palindromic Repeats.

Why is CRISPR described as a 'bacterial immune system'?

It allows the bacterium to 'remember' past viral infections and specifically destroy the same virus upon re-exposure.

What is the 'gut virome'?

The community of bacteriophages (mostly coliphages) living within the mammalian intestinal tract.

List three areas of human health modulated by the gut bacteriophage community.

1. Digestion 2. Immune system 3. Mental health.

In the gut, how can phages change the host population distribution?

By infecting and killing specific bacterial strains while leaving others to thrive.

What is 'transcytosis' in the context of gut phages?

The process by which phages are taken up by gut cells and potentially stimulate the immune system.

True or False: Viruses can contain both DNA and RNA in their genome.

False (They contain either DNA or RNA, never both).

Which specific bacterium is infected by bacteriophage T2?

E. coli.

Describe the structural components of the T4 bacteriophage tail.

It consists of a sheath, a base plate, and tail fibers.

What determines whether a temperate phage enters the lytic or lysogenic cycle?

Environmental cues and the health/survival status of the host cell.

Tobacco Mosaic Virus (TMV) is an example of a _____ virus.

Plant.

The integrated phage lambda in E. coli O157:H7 provides a protein that affects which host structure?

The cell envelope.

Which integrated viral genome provides the human protein Syncytin-2 for placental fusion?

HERV-FRD.

What is the characteristic appearance of a tobacco leaf infected with TMV?

Discoloration and the presence of spores/spots.

What happens to the measles virus as it exits a human cell?

It 'buds' out, taking a part of the host's cell membrane to form its envelope.

In the context of viral forms, what occurs during the 'intracellular replication complex' phase?

The virus is active, directing host enzymes to replicate its genome and assemble new virions.

Explain why viruses are technically considered 'non-living' outside a host.

They are inert particles that lack metabolism and the ability to reproduce independently.

The circular ssRNA of a viroid is replicated by which host enzyme?

Host RNA polymerase.