Chapter 6 - Viral Structure

What is virology?

The discipline that studies viruses, infectious agents unique in their simple, acellular organization and pattern of multiplication

What are bacteriophages?

Viruses that infect bacteria (also called phages for short)

What are phages?

Short term for bacteriophages - viruses that infect bacteria

What organisms can viruses infect?

All cell types including bacteria (bacteriophages/phages), archaea (fewer identified), and eukaryotic organisms (plants, animals, protists, and fungi)

What is the typical size range of virions?

From about 20 nm in diameter to about the same size as a rod-shaped bacterial cell (1.5 × 0.5 μm)

What are the smallest viruses compared to in size?

Slightly larger than ribosomes

What are the largest known viruses called and how can they be viewed?

Mimiviruses, which can be seen with light microscope

How must most virus particles be viewed?

With electron microscopes

What is nucleic acid in viruses?

DNA or RNA (single or double stranded) that contains genetic information for viral replication - found in all viruses

What is a capsid?

Protein coat made of protomers that protects viral nucleic acid and aids in transfer between host cells - found in all viruses

What is a nucleocapsid?

The combination of nucleic acid and capsid - the basic viral structure found in all viruses

What is a viral envelope?

Lipid membrane derived from host cell that protects nucleocapsid and aids in attachment and entry - only found in enveloped viruses

What are spikes/peplomers?

Viral proteins projecting from envelope involved in attachment to host cells and enzymatic activity for entry/exit - only on enveloped viruses

What are capsomers?

Ring/knob-shaped assemblages of protomers that serve as building blocks of icosahedral capsids - only in icosahedral capsids

What are enveloped viruses?

Viruses that have a lipid membrane surrounding their nucleocapsid, with envelope coming from host cell membranes

Where do viral envelopes come from?

Host cell membranes including plasma membrane, endoplasmic reticulum, Golgi apparatus, or other organelle membranes

What components of viral envelopes come from the host vs virus?

Envelope lipids and carbohydrates are acquired from host, while envelope proteins are coded by viral genes

What are nonenveloped (naked) viruses?

Viruses that lack a membrane and consist only of nucleocapsid

Are viral genomes always DNA like cellular organisms?

No, viruses employ all four possible nucleic acid types

What are the four types of viral nucleic acids?

Double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), and double-stranded RNA (dsRNA)

What is the most common type of DNA virus genome?

Double-stranded DNA (dsDNA), which may be linear or circular

Give examples of ssDNA viruses

φX174 and parvovirus

What is the most common RNA virus type?

Single-stranded RNA (ssRNA)

Give examples of ssRNA viruses

Coronaviruses, TMV, rabies, HIV

How many dsRNA viruses exist?

Relatively few viruses use dsRNA

What are segmented genomes?

Multiple RNA pieces where each segment often codes for one protein, found in some RNA viruses

What is the first step of viral replication?

Attachment (Adsorption) - specific interactions between viral surface ligands and host cell receptors that determines host specificity and tissue tropism

What is the second step of viral replication?

Entry into Host - viral genome or nucleocapsid enters cytoplasm through membrane fusion, endocytosis followed by uncoating, or direct injection

What are the three methods of viral entry?

Membrane fusion (enveloped viruses), endocytosis followed by uncoating, or direct injection of nucleic acid through membrane

What is the third step of viral replication?

Synthesis - production of viral nucleic acids and proteins, organized into early, middle, and late gene expression

How do DNA viruses differ from RNA viruses in synthesis?

DNA viruses can use host machinery; RNA viruses must carry or synthesize their own replication enzymes

What is the fourth step of viral replication?

Assembly - self-assembly of nucleocapsids from viral components, may involve complex subassembly lines and scaffolding proteins

What is the fifth step of viral replication?

Release - either by lysis (host cell destruction) or budding (gradual release while host may survive)

What are viral receptors?

Specific molecules on host cell surfaces that viral ligands bind to for attachment, usually proteins or glycoproteins that serve important functions for the host cell

What determines viral host range and tissue tropism?

Receptor specificity

What is the role of capsid/envelope proteins in viral replication?

Critical for attachment (step 1) and entry (step 2) - they contain ligands that bind to host cell receptors and facilitate penetration

What are the two common methods for virion release?

Lysis (host cell destruction through viral enzymes) and budding (gradual release where nucleocapsid becomes surrounded by host membrane)

What is lysis in viral release?

Host cell destruction through viral enzymes that puncture membranes and degrade cell walls, common in bacteriophages and some animal viruses

What is budding in viral release?

Gradual release where nucleocapsid becomes surrounded by host membrane containing viral proteins, common in enveloped viruses

What are virulent phages?

Phages that begin multiplying immediately upon infection and lyse the host cell (lytic cycle only)

Give an example of a virulent phage

T4 phage

What are temperate phages?

Phages that have two options - can multiply and lyse host (lytic cycle) OR remain dormant within host (lysogenic cycle)

Give an example of a temperate phage

Lambda phage

What is lysogenic conversion?

Process by which a temperate phage changes the phenotype of its host, often involving alteration of surface characteristics

Give an example of lysogenic conversion

Epsilon phages infecting Salmonella change enzymes involved in lipopolysaccharide construction, eliminating receptor for epsilon phage and conferring immunity

What is an acute infection?

Cytocidal infection resulting in cell death and lysis

What is a latent infection?

Persistent infection where viral components are present but host is not harmed; can be activated later

What is a chronic infection?

Persistent infection with slow release of virus without immediate cell death

What is transformation in viral infection?

Infection causes host cell to become malignant (cancer cell)

What is an oncovirus?

Virus that can transform normal cells into malignant cells, potentially causing cancer

How do oncoviruses cause cancer?

They may activate host proto-oncogenes, insert oncogenes, or inactivate tumor suppressor proteins

What happens during plaque formation?

Infected cells lyse and release progeny phages that infect nearby cells, creating a clear area (plaque) in the bacterial lawn where cells have been destroyed

What does each plaque theoretically represent?

One infectious virus particle

What is infectious dose?

The number of viral particles required to establish infection in a host

What is lethal dose?

The number of viral particles required to kill the host

What are prions?

Proteinaceous infectious particles composed only of protein (no nucleic acid) that are abnormally folded versions of normal cellular proteins causing progressive neurodegenerative diseases

How do prions "replicate"?

By converting normal cellular prion protein (PrPᶜ) into abnormal form (PrPˢᶜ) through direct contact, with abnormal protein acting as template

What happens after prion conversion?

The abnormal proteins aggregate, leading to disease

Give examples of human prion diseases

Creutzfeldt–Jakob disease, kuru, fatal familial insomnia, or Gerstmann-Strässler-Scheinker syndrome

What is the prognosis for prion diseases?

All cause progressive brain degeneration and death with no effective treatment currently available

What is a protomer?

Protein subunit that makes up viral capsids, with thousands self-assembling to form the capsid

What missing components distinguish viruses from cells?

Ribosomes for protein synthesis, mechanism for generating ATP, and cytoplasm

What are helical capsids?

Capsids shaped like hollow tubes with protein walls, can be rigid or flexible

What example illustrates helical capsid structure?

Tobacco mosaic virus (TMV) with RNA genome wound in spiral within groove formed by protein subunits

What influences helical capsid size?

Diameter determined by size, shape, and interactions of protomers; length determined by size of viral genome

What is an icosahedron?

Regular polyhedron with 20 equilateral triangular faces and 12 vertices - most efficient way to enclose space

What are pentamers (pentons)?

Capsomers composed of five protomers, found at vertices of icosahedral capsids

What are hexamers (hexons)?

Capsomers composed of six protomers, found on edges and faces of icosahedral capsids

What are complex capsids?

Capsids that don't fit icosahedral or helical categories, found in poxviruses and large bacteriophages

What is binal symmetry?

Symmetry where viral head is icosahedral and tail is helical, seen in T-even phages

What is the structure of T4 phage?

Icosahedral head containing DNA, collar, central hollow tube, surrounding sheath, and complex baseplate with fibers

What are the components of poxvirus structure?

Ovoid to brick-shaped exterior with core (biconcave disk with DNA and proteins), two lateral bodies containing viral enzymes, surrounded by outer envelope

What are viral enzymes associated with?

Envelope, capsid, or carried within capsids, usually involved in nucleic acid replication

What do RNA viruses often carry?

Enzyme that synthesizes RNA using RNA template since host cells lack this capability

What was the one-step growth experiment?

1939 experiment by Delbrück and Ellis showing viral multiplication has latent period (no virions released) followed by rise period (rapid release)

What is the eclipse period?

Early part of latent period where no virus particles are present in infected cells - viruses are "concealed" within host

What happens during the eclipse period?

Infecting virions disappear inside cell and viral components are synthesized before assembly into complete virions

What determines viral tropism?

Distribution of specific receptors on different cell types and tissues

How do plant viruses differ in attachment?

No identified receptors - require cell damage for entry, often achieved by plant-eating insects carrying virions

What are the three modes of animal virus entry?

Fusion of viral envelope with plasma membrane, entry by endocytosis, or release of nucleic acid into cytoplasm

What triggers uncoating in endosomes?

Low pH and endosomal enzymes

What are viral replication complexes?

Membranous structures formed by reorganizing host cell membranes to enclose machinery for genome replication, transcription, and protein synthesis

What are viroplasms?

Areas of concentrated viral genomes, mRNAs, and proteins in cytoplasm not enclosed by membranes, also called virus factories

What are early, middle, and late proteins?

Classification based on when genes are expressed during infection - early (takeover), middle (replication/activation), late (assembly/release)

What are nonstructural (NS) proteins?

Proteins involved in viral replication but not incorporated into virion

What are structural proteins?

Proteins present in the mature virion

What is a prohead (procapsid)?

Preliminary head structure assembled with aid of scaffolding proteins that are degraded or removed after assembly

What is the packasome?

Complex of proteins including portal protein and terminase enzyme that moves DNA into prohead using ATP

What are the two most common viral release mechanisms?

Host cell lysis and release by budding

What causes lysis in bacteriophages?

Viral proteins that puncture host membranes and degrade peptidoglycan, causing osmotic stress

What is the novel release mechanism in some archaeal viruses?

Seven-sided pyramid structures form near cell envelope, puncture it and open like flower petals to release virions

What is concurrent with envelope formation?

Virion release in enveloped viruses

What is a matrix (M) protein?

Protein that attaches to plasma membrane and aids in budding in several virus families

What membranes can form viral envelopes?

Plasma membrane (most common), endoplasmic reticulum, Golgi apparatus, and other internal membranes

How do some viruses avoid extracellular phase?

Move directly cell-to-cell through plasmodesmata (plants) or via actin tails (vaccinia virus)

What is lysogeny?

Relationship between temperate phage and host where virus remains within host without destroying it

What is a prophage?

Form of virus that remains within host, either integrated into bacterial chromosome or free in cytoplasm

What are lysogens?

Infected bacteria in lysogenic relationship

What are two characteristics of lysogenic bacteria?

Cannot be reinfected by same virus (immunity to superinfection) and prophage is replicated and inherited

What is induction?

Process where prophage initiates synthesis of phage proteins and assembly of new virions, ending lysogenic cycle