Biology – 261

Chapter 9
- Overview
o Virus: genetic element that cannot replicate independently of a living (host) cell
 Not considered cells because need host to replicate
 Structure – nucleic acid surrounded by protein coat (capsid)
o Virology: the study of viruses
o Virus particle: extracellular form of a virus; allows virus to exist outside host and
facilitates transmission from one host cell to another
o Virion: the infection particle; the nucleic acid genome surrounded by a protein coat and,
in some cases, other layers of material – completed infected virus
o Viruses are very specific  only infect certain things because of inceptors on protein
coat
o Viruses that infect bacterial cell doesn’t go all the way in cell, but it does in animal cell
o Viruses requires host cell to reproduce by using hosts machinery to reproduce and
create protein coating
- General propertied of viruses
o Viral genomes
 Either DNA or RNA genomes (some use both as their genomic material at different
stages in replication cycle, one type of nucleic acid, single or double stranded)
 Some circular, but most linear
o Viral hosts and taxonomy
 Viruses can be classified on the basis of the hosts they infect
 Bacterial viruses (bacteriophages
 Animal viruses
 Plant viruses
 Archaeal viruses
 Viruses come in many shapes and sizes
 Measured in nanometers
- Nature of the virion
o Viral structure
 Capsid: the protein shell that surrounds the genome of a virus particle
 Composed of a number of protein molecules arranged in a precise and
highly repetitive pattern around the nucleic acid
 Capsomer: subunit of the capsid
 Smallest morphological unit visible with an electron microscope
 Nucleocapsid: complete complex of nucleic acid and protein packaged in the virion
 Bacteriophage
 Enveloped virus: virus that contain addition layers around the nucleocapsid; when
a virus buds out of its host cell it takes with it part of the cytoplasmic membrane
 Primarily seen in animal viruses
 Either naked (lyse) or enveloped (bud - outer membrane)
o Nucleocapsids of viruses constructed in highly symmetric ways
 Helical symmetry: rod-shaped viruses (tobacco mosaic virus)
 Length of virus determined by length of nucleic acid
 Width of virus determined by size and packaging of protein subunits
 Icosahedral symmetry: spherical viruses
 Most efficient arrangement of subunits in a closed shell
o Enveloped viruses: have membrane surrounding nucleocapsid; lipid bilayer with
embedded proteins
 Make initial contact with host cell (envelope)
 Envelope comes from host cell cytoplasmic membrane so its lipid bilayer – lipid
may contain proteins that are spikes flu virus
o Complex viruses: virions composed of several parts, each with separate shapes and
symmetries
  Bacterial viruses contain complicated structures
 Lcosahedral heads and helical tails
 Many bacteriophages have complex shape because multiple parts
o Some virions contain enzymes critical to infection
 Lysozyme – breaks down PG cell walls
 Some viruses may carry useful info for cell example
 Nucleic acid poly
 Neuraminadases: enzyme that cleaves gycosidic (sugar) bonds; allows liberation
of viruses from host (helps spread of viruses)
 Bacterial viruses use lysozyme to get into cell – reverse transcription
- The virus host
o Virus replicate only in certain types of cells or in whole organism
o Bacterial viruses are typically easiest to grow; model systems
o Animal viruses (and some plant viruses) can be cultivated in tissue or cell cultures
o Plant viruses typically are most difficult because study often requires growth of whole
plant
o Note: viruses infect specific hosts so in order to grow virus you must first grow host
- Quantification of viruses
o Titer: number of infectious units per volume of fluid
o Plaque assay: analogous to the bacterial colony; one of the most accurate ways to
measure virus infectivity
 How you determine the number or titer
 Plaques are clear zones that develop on lawns of host cells
 Each plaque results from infection by a single virus particle
 Plaque = 1 virus
 Lawn can be bacterial or tissue culture
- General features of virus replication
o The phases of viral replication
 Attachment (adsorption) of the virus to a susceptible host cell
 Entry (penetration) of the virion or its nucleic acid
 Synthesis of the virus nucleic acid and protein by cell metabolism as redirected by
virus
 Assembly of capsids and packaging of viral genomes into new virions (maturation)
 Release of mature virions from host cell
o Overview of steps above
 Virus attaches, virus gets inside, phage inject nucleic acid into bacteria and capsid
stays on outside of host, animal virus are taken completely into host cell and must
be uncoated two release viral nucleic acid, once inside, virus is able to use host
cell enzymes and macromolecules to make new viruses, individual nucleic acids
and capsules are made and released from host cells, to leave host, virus can
either lyse host or bud which requires an envelope
 Note:
 Replicates in cytoplasm
 Bacteria = injects DNA
 Animal = whole virus into the host and has to be uncoated to be replicated
(replicated in nucleus)
o Transcription and translation occur for both
 When animal virus is taken in cell, it must get rid of the capsid
o Virus replication typically characterized by a one-step growth curve
o Latent period: eclipse + maturation
o Burst size: number of virions released
 Actual number of viruses released after 1 cycle
o Note: with bacterial growth curve was 4 phases, viruses only have one step because
virus is inside the host cell
- The viral attachment and penetration
 o Bacteriophage T4: virus of E. coli – example of one of the most complex penetration
mechanisms known (lytic bacteriophage that infects its host)
 Virions attach to cells via tail fibers that interact specifically with polysaccharides
on E. coli cell envelope
 Tail fibers retract and tail core makes contact with E. coli cell wall
 Lyzozyme-like enzyme forms small pore in peptidoglycan
 Tail sheath contracts and viral DNA passes into cytoplasm
- Production of viral nucleic acid and protein
o David Baltimore, Howard Temin, and Renato Dulbecco discovered retroviruses
transcriptase
 Shared 1975 Nobel Prize for Physiology or Medicine
o Baltimore developed classification scheme for viruses based on relation of viral genome
to its mRNA
 Baltimore system used o name viruses which is very different from bacteria;
viruses do not have a genus and species
 7 groups based on DNA/ RNA
o Once a host has been infected, new copies of the viral genome must be made and virus-
specific proteins synthesized in order for the virus to replicated
o Generation of mRNA occurs first
o Typically viral genome serves as template for viral mRNA
o In some RNA viruses, viral RNA itself is the mRNA
o In some cases essential transcriptional enzymes are contained in the virion
o Notes:
 Naked virus = inject DNA
 Enveloped virus = membrane fusion (enveloped = membrane)
 Phagocytosis  cell eating virus; naked and enveloped
 DNA = 1 x copies
2 x copies with DNA poly from host and undergo transcription and
translation to make viral proteins
 RNA = + (sense strand) mRNA  translation happens
- (Antisense) has to be copied into = strand before translation
 Retro = RNA  DNA (enter host and called a provirus and can now cause a
mutation  why can cause cancer
o Nomenclature used to describe mRNA is used to the configuration of the genome of a
single-stranded DNA or RNA virus (mRNA is said to be in plus (+) configuration; its
complement is in minus (-) configuration)
 Positive strand RNA virus: single stranded RNA genome with the same orientation
as its mRNA
 Negative strand RNA virus: single stranded RNA genome with complementary
orientation as its mRNA
o Retroviruses: animal viruses responsible for causing certain types of cancers and
acquired immunodeficiency syndrome (AIDS)
 Class VI and VII transcriptase (RNA  DNA)
- Overview of bacterial viruses
o Bacteriophages are very diverse
o Best studied bacteriophages infect enteric bacteria
 E. coli, salmonella, enterica
o Most contain dsDNA genomes
 Most common types of bacteria with dsDNA lamdda and T4
o Most are naked, but some posses lipid envelopes
o They are structurally complex, containing heads, tails, and other components
o Viral life cycle
 Virulent mode: viruses lyse host cells after infection
 Temperate mode: viruses replicate their genomes in tandem with host genome
and without killing host (lambda)
  Virus can also be lylic
 Lysogenic: makes prophage
- Viral replication: Virulent bacteriophages
o Life cycle= lytic cycle  attaches to host cell and penetrates it by injecting its DNA;
thus causes host DNA to break into small pieces and synthesizes new copies of DNA
(biosynthesis); now phages are assembled into virions  now ready to release phages
and cell lyse
- Temperate bacteriophages, lambda, and P1
o Bacteriophage Lambda
 Linear, dsDNA genome
 Upon penetration, DNA ends base-pair forming the cos site, DNA ligates and forms
double stranded circle
 When lambda is lysogenic, it’s DNA integrates into E coli chromo at the lambda
attachment
 Lambda is a double stranded DNA lysogenic bacteriophage
- Viral replication: temperate bacteriophage
o Two life cycles: lytic cycle, lysogenic cycle
 Lytic: similar to virulent; attaches to host and injects DNA which forms oxygen
now can go to either cycle; if stays in lytic it will cause host DNA to synthesis viral
components then assembled into virions; released and cell lyses
 Lysogenic: when DNA forms oxygen and viral DNA integrates with host DNA by
recombination; viral DNA now called prophage proteins are repressed and
prophage is copied when bacteria reproduces; prophage is cut off by induction via
UV light, spontaneously or other  now phage can enter lytic cycle
- Overview of animal viruses
o Entire virion enters the animal cell and it must be uncoated before replication occurs
unlike pro
o Eu cells contain a nucleus, the site of replication for many animal viruses
o Animal viruses contain all known modes of viral genome replication
o Many more kinds of enveloped animal viruses than bacterial viruses exist
 As animal viruses leave host cell, they can remove part of host cell’s lipid bilayer
for their envelope
o Notes:
 Vary on type of nucleic acid they posses and whether they are naked or enveloped
each difference = different life cycles
 Naked: no enveloped and bin to surface and inject DNA
 Major difference between phages and animal viruses: capsid of phages is left
outside the host following penetration and with the animal viruses the entire virus
is taken into the host and must uncoded to released the nucleic acid
 Many of the animal viruses bud out of the host cell sot hey will have an envelope
which comes out the cytoplasmic membrane of host cell
o Consequences of virus infection in animal cells
 Persistent infections: release of virions from host cell does not result in cell lysis
 Infected cell remains alive and continues to produce virus indefinitely
 Virus buds out without lysing host
 Latent infections: delay between infection by the virus and lytic events
 Virus enters host chromos and known as proviruses and can go into lytic
cycle
 Transformation: conversion of normal cell into tumor cell
- Retroviruses
o Retroviruses: RNA viruses that replicate through a DNA intermediate
 Enveloped viruses
 Contain a reverse transcriptase (copies information from its RNA genome into
DNA), intergrase and protease
 Virion contains specific tRNA molecules
 o Notes:
 Retro = backwards
 Copies single stranded RNA into double stranded DNA which then integrates into
host chromos and becomes provirus
 Transcription DNA  RNA
o Retroviruses have a unique genome
 Two identical ssRNA molecules of the plus (+)
 Contain specific genes
 Gag: encode structural proteins
 Pol: encode reverse transcriptase and integrase
 Env: encode envelope proteins
 Note:
 Plus can be translated right away
 Viral RNA carries the genes that are unique to the virus
o Process of replication of a retrovirus
 Entrance into the cell
 Removal of virion envelope at the membrane
 Reverse transcription of one of the two RNA genomes
 Integration of retroviral DNA into host genome
 Transcription of retroviral DNA
 Assembly and packaging of genomic RNA
 Budding of enveloping virions; released from cell
- Defective viruses: can replicate but doesn’t have one of its capsid genes so it relies on P2 for
the major capsid protein
o Require other virus (helper virus) to provide some function
 Some rely on intact virus on same type
 Satellite viruses: defective viruses for which no intact version exist; rely on
unrelated viruses as helpers
- Viroids
o Viroids: infectious RNA molecules that lack a protein coat
 Small, circular, ssRNA molecular
 Smallest known pathogens
 Cause a number of important plant disease
 Do not encode proteins; completely dependent on host – encoded enzymes
o Only RNA and are infectious
o Infect plants and cause disease
- Prions: infections proteins whose extracellular form contains no nucleic acid
o Known to cause disease in animals (transmissible spongiform encephalopathy – Mad
Cow)
o Host cell contains gene (PrnP) that encodes native form of prion protein that is found in
healthy animals
 All mammalian cells contain PrnP
o Prion misfolding results in neurological symptoms of disease (resistance to proteases,
insolubility, and aggregation)
o Cause prion proteins to change shape and cause plaques in brain only protein not
protein not cells or any cells, or any nucleic acid
o Prion disease occurs by three distinct mechanisms (disease in animals)
 Infectious prion disease: pathogenic form of prion protein is transmitted between
animals or humans
 Sporadic prion disease: random misfolding of a normal. Healthly prion protein in
an uninfected individual
 Inherited prion disease: mutation in prion gene yields a protein that changes more
often into disease-causing form
o Do not reproduce instead cause other cellular proteins of the same type of misfold into
infectious form
o Usually PrnP folds into functionally form (2 different folds)
o Many prions = multimers (more harmful)