ch 6 - viruses, virions, prions

virus

noncellular particles; obligate intracellular parasites with a definite size, shape, and chemical composition. non-living bc no metabolism, doesn’t grow, no cell membrane, and needs help to reproduce

virus

what is the most abundant microbe on earth? these also play a role in the evolution of bacteria, archaea, and eukarya

virus size

ultramicroscopic, 20 nm (size of a protein) to 450 nm in diameter. requires an electron microscope to see. filterable particles

properties of viruses

• inactive macromolecules outside the host cell and active only inside the host cell (but can be transferred from individuals while inactive)

• capsid + nucleic acid core

• genome is RNA or DNA but not both

• double stranded or single stranded

• virus surface has high specificity for attachment to host cell

how do viruses survive

• multiply by taking control of host cell’s genetic material and regulating the synthesis and assembly of new viruses

• lack enzymes for most metabolic processes

• lack machinery for synthesizing proteins

• invade host cell, destroy dna, make ribosome produce viral DNA (requires host)

megavirus and pandavirus

• largest viruses: avg 500-1000 nm (20-50x bigger than the avg virus)

• these can be seen under a light microscope

• megavirus and pandavirus

viral structure

• lack cell membrane

• no resemblence to cells

• no protein synthesizing machinery

• covering (capsid and/or envelope)

• central core (nucleic acid = DNA or RNA)

  • some have matrix proteins enzymes (not all viruses)

crystalline nature

viral molecular structure is regular, repeating molecules that result in a crystalline appearance. when purified, many form large aggregates or crystals

capsids

• all viruses have protein coats that enclose and protect the nucleic acid

• made of identical protein subunits called capsomers (produce facets of icosahedral virus)

• helical or icosahedral structure

• some viruses have envelope, others are naked

nucleocapsid

capsid together w nucleic acid (RNA or DNA)

spike

part of viral envelope that aids in entry and exit of host cell (H spike attachment for entry) and N spike for exit

• spike proteins are mutating → antibodies won’t bind

helical capsid

continous helix of capsomers forming a cylindrical nucleocapsid (slinky). can be naked or enveloped

icosahedral capsid

3D symmetrical polygon, 20 sides and 12 evenly spaced corners. can be naked or enveloped.

• during assembly, the nucleic acid is packed into the center of the icosahedron, forming the nucleocapsid

helical nucleocapsid assembly

• helical capsids

• rod shaped capsomers assemble into hollow discs

• the nucleic acid is inserted into the center of the disc

  • elongation of the nucleocapsid progresses from both ends, as the nucleic acid is coiled inside

envelope

• consists of a phospholipid bilayer stolen from the host

• Hemagglutinin spike for entry (attachment)

• Neuraminidase spike for exit

• sometimes matrix proteins for maintaining viral shape

rotavirus

example of naked icosahedral virus

herpes simplex

example of enveloped icosahedral virus (cold sores, low virulence, giant cells)

virus envelope structure

• mostly in animal viruses, stolen from host when the virus leaves the host cell

• exposed proteins on the outside of the envelope, called spikes, are essential for attachment of the virus to the host cell

• Hemagglutinin spikes and Neuraminidase spikes

function of the capsid/envelope

• protects the nucleic acid when the virus is outside of the host cell

• helps the virus bind to a cell surface and assists the penetration of the viral DNA or RNA into a suitable host cell

• most animal/human viruses contain this

baltimore classification

a system that groups viruses into 7 classes based on the type of genome (DNA or RNA) and how they replicate and produce mRNA

• enveloped/naked

• DNA/RNA

• ss or ds RNA/DNA

complex virus

atypical virus (not icosahedral or helical, sometimes more structures or elaborate design)

• poxvirus - very large, dense layer of lipoproteins

• bacteriophages - viruses that only infect bacteria

poxvirus

• atypical/complex virus

• lacks capsid

• covered by dense layer of lipoproteins

• extremely large

bacteriophages

• atypical/complex virus

• has a polyhedral nucleocapsid w a helical tail and attachment fibers

• “consuming bacteria”; doesn’t parasitize plants, animals, protozoa

viral nucleic acids

• viral genome - either DNA or RNA but never both

• carries genes necessary to invade host cell and redirect cell’s activity to make new viruses

• number of genes varies for each type of virus - few to hundreds

DNA viruses

• usually double stranded but may be single stranded

• circular or linear

RNA viruses

• usually SS, may be DS, may be segmented into separate RNA pieces rather than 1 giant RNA

• uses host cell ribosome to do all this, but does make its own polymerase

• ssRNA genomes can be positive sense or negative sense RNA

positive sense RNA

ssRNA genomes in RNA virus ready for immediate translation (ribosome can only read it if it’s positive sense)

negative sense RNA

ssRNA genome of RNA virus must be converted into proper form, bc ribosome can only read if its a positive sense

enzymes for viral replication

• polymerases - synthesize DNA or RNA

• replicases (RNA dependent RNA polymerase) = copies RNA from RNA

• reverse transcriptase - synthesis of viral DNA from RNA (HIV virus) to splice into our DNA

families

italicized and given suffix -viridae

there’s 104 of them

genera

italicized and end in -virus

there’s 505 of them

virus nomenclature

• type of capsid, nucleic strand #, presence and type of envelope, viral size, area of the host cell in which the virus multiplies

• microscopic appearance (rhabdoviruses)

• anatomical/geographic areas (adrenoviruses, hantaviruses)

• effects on the host (lentiviruses)

• acronyms blending several characteristics (picornaviruses)

modes of viral replication

• adsorption

• penetration

• uncoating

• synthesis

• assembly

• release

adsorption

binding of virus to specific molecules on host cell receptor sites on the host cell membrane (hemagglutinin spike protein for entry); naked or enveloped

penetration

genome enters the host cell

uncoating

the viral nucleic acid is released from the capsid

synthesis

viral components are produced

assembly

new viral particles are constructed. mature virus particles are constructed from the growing pool of parts

• capsid is first laid down as an empty shell, receptacle for the nucleic acid strand

release

assembled viruses are released by budding (exocytosis) or cell lysis

host range

• spectrum of cells a virus can infect

• hepatitis b = human liver cells

• poliovirus = primate intestinal and nerve cells (paralysis)

• rabies = various cells of many mammals

penetration/uncoating

• animal viruses must penetrate the cell membrane of the host cell and deliver the viral nucleic acid into its interior

• fusion (enveloped) - viral envelope fuses directly w host membrane by rearrangement of lipids

• endocytosis (enveloped or naked) - entire virus is engulfed and enclosed in vacuole or vesicle, then uncoated

fusion

penetration/uncoating of envelope viruses - viral envelope fuses directly w host membrane by rearrangement of lipids. virus is uncoated during fusion

endocytosis

enveloped or naked virus penetration/uncoating - entire virus is engulfed and enclosed in vacuole or vesicle, then uncoated → viral nucleocapsid or nucleic acid is released

nucleus

where are DNA viruses replicated and assembled

cytoplasm

where are RNA viruses replicated and assembled?

budding (exocytosis)

• release for enveloped viruses

• nucleocapsid binds to membrane which pinches off and sheds the viruses gradually

• cell is not immediately destroyed

• host cell is making spikes @ membrane, destroying host cell and chromosome. producing viral particles

cell lysis

release of nonenveloped and complex viruses. cell ruptures and dies, releasing viruses

cytopathic effects

cell dmg altering microscopic appearance.

• disorientation of individual cells

• gross changes in shape or size (rounding up)

• intracellular changes (inclusion bodies, syncytium)

  • inclusion bodies - clumps that form inside infected cells

  • syncytium - several cells fuse together, forming a giant mutlinucleated cell

persistent infections

• cell harbors the virus and is not immediately lysed (latency)

• can last weeks or host’s lifetime; several can periodically reactivate - chronic latent state

• measles hidden in brain cells for many years

• herpex simplex virus - cold sores and genital herpes

• herpes zoster virus - chickenpox and shingles (latent)

oncoviruses

some animal viruses enter the host cell and splice themselves into our genome, turning into a transformed cell (increased rate of growth, alterations in chromosomes). transformations = rapidly producing cell = tumor

• papillomavirus = cervical cancer

• epstein-barr virus = burkitt’s lumphoma

bacteriophage replication

• only the nucleic acid enters the cytoplasm, uncoating isn’t necessary

• release is a result of cell lysis induced by viral enzymes and accumulation of viruses - lytic cycle (full on destruction of bacteria)

• multiplication of bacterial viruses is similar to stages of animal virus

steps in phage replication

• adsorption - binding of virus to specific molecules on host cell

• penetration - genome enters host cell

• replication - viral components are produced

• assembly - viral components are assembled

• maturation - completion of viral formation

• lysis and release - the lytic cycle involves full completion of viral infection thru lysis and release of virions

• sometimes lysogeny - DNA incorporated into the host’s chromosome (genetic material)

lytic cycle

bacteriophage takes over cell, makes copies of itself, bursts the cell open to release new viruses

• adsorption, penetration, replication, assembly, maturation, lysis and release

• sometimes converts to lysogenic cycle

lysogenic cycle

sometimes the lytic cycle and converts to this, and can convert back to lytic cycle

• virus inserts viral DNA into the host DNA (chromosome) and copies itself when the cell divides

• viral DNA is duplicated along w the regular genome

• latent time bomb

lysogeny

• not all phages complete the lytic cycle

• some DNA phages, called temperate phages, undergo adsorption and penetration but don’t replicate (dormant long time)

• viral genome inserts into bacterial genome and becomes an inactive prophage - cell isn’t lysed

• prophage is retained and copied during normal cell division resulting in the transfer of temperate phage genome to all host cell progeny - lysogeny

• induction (turns against the host cell) can occur → enter lytic phase

temperate phage

DNA phage (bacteriophage) that can choose btwn the lytic (destroy) and lysogenic (hide) cycle

lysogenic conversion

• phage genes in the bacterial chromosome can cause the production of toxins or enzymes that CAUSE pathology (conversion)

• lysogeny → spread of the virus w/o killing host cell

• ex: not originally pathogenic but viral infection made it pathogenic

  • corynebacterium diptheriae

  • vibrio cholerae

  • clostridium botulinum

in vitro

• cell or tissue cultures

• cultured cells support viral replication and permit observation of cytophathic (damaging) effects

  • disorientation of individual cells

  • gross changes in shape or size (rounding up)

  • intracellular changes (inclusion bodies, syncytium)

in vivo

• “in the living”

• bird embryos - intact and self sustaining unit, sterile, nourishing, supports viral replication

• live animal inoculation - animal is injected w viral preparation or specimen

medical importance of viruses

• most common cause of acute infections

• billions of viral infections annually

• some have high mortality rates

• participates in earth’s ecosystem (evolution of archaea, eukarya, prokaryotes)

prions

• misfolded proteins, contain no nucleic acid (RNA/DNA)

• extremely resistant to sterilization techniques

• transmissible spongiform encephalopathies (TSEs) = fatal neurodegenerative diseases

• mad cow disease

• no cure

mad cow disease

• caused by misfolded proteins w no nucleic acid

• Creutzfeldt-Jakob syndrome (CJS) in humans

• bovine spongiform encephalopathies (BSE)

how do prions work

prions turn alpha helices of protein to turn into beta pleated sheets → causes lesions on brain when it changes

satellite viruses

• dependent on other viruses for replicaiton

• adeno-associated virus: replicates only in cells infected w adenovirus

• delta agent: naked strand of RNA expressed only in the presence of hepatitis B virus

viroids

short pieces of RNA, no protein coat; only been identified in plants