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220 Cards in this Set
- Front
- Back
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What is a virus?
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Small, obligate intracellular parasite
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What is a viroid?
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Plant pathogen, RNA only, does NOT code protein
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How do viroids replicate?
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Rolling circle mechanism
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What was the first virus discovered?
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Tobacco mosaic virus
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What was the first human virus identified?
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Yellow fever
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How small are viruses?
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10-100nm
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What system do we use to classify viruses?
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Baltimore System
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Baltimore I?
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dsDNA
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Baltimore II?
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ssDNA (+)
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Baltimore III?
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dsRNA
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Baltimore IV?
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+ ssRNA --> -RNA
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Baltimore V?
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- ssRNA
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Baltimore VI?
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+ ssRNA --> - DNA ---> dsDNA
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What kind of genome would a virus NOT have?
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- DNA
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Name 4 methods to study virus structure:
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EM
cryoEM X-ray crystallography NMR |
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Name 3 functions of the virion:
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-Protection of genome
-Delivery of genome -Interactions with host |
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What is a structural subunit?
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unit from which capsids/nucleocapsids are made
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What is a morphological unit?
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surface structures seen by EM
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What is a virion?
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a complete infectious particle
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Name the 3 forms of capsids:
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-helical
-icosahedral -complex |
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Name three examples of viruses with helical capsids:
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-Tobacco mosaic virus
-Sendai virus -VSV |
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What are the parameters used to describe helical capsids? (5)
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mu - nbr. of structural units/turn of helix
rho - rise/turn P - pitch diameter length |
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What is mu for tobacco mosaic virus?
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16.3
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What does pitch equal?
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mu x rho
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How many faces does an icosahedral capsid have?
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20
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What are the axes of symmetry of an icosahedron?
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2, 3, and 5-fold
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What is the triangulation number?
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nbr. of asymmetric units/face
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Name 6 icosahedral viruses!!!
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-canine parvovirus
-poliovirus -simian virus 40 (papova) -herpes -adenovirus -reovirus |
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Name a tiny virus where T=1:
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canine parvovirus
60 x VP2 |
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What is the structure of poliovirus?
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T=3
VP1, 2, 3 and 4 plateaux and canyons beta-barrel jellyroll |
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What structure is conserved in icosahedral capsid proteins?
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beta-barrel jelly rolls!!!
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What icosahedral virus is so fab it has 2 layers?
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Reovirus
outer - T=13, VP7 trimers inner - T=2, VP3 monomers |
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Herpes is made up of hexons and pentons of what protein? EH?
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VP5
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Simian Virus 40 is made up of what units? How many of them? What is its triangulation number?
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72 pentamers
each made of 5 x VP1 T=7 |
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Which virus is superbig? 12 pentons and 240 hexons, where T=25
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adenovirus
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Name a virus with a complex capsid:
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HIV-1
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What kind of capsid does HIV-1 have, exactly?
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fullerance cone
made up of hexons and pentons narrow end 5 pentons wide end 7 pentons |
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What are three methods of packaging viral genomes?
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1) direct contact with capsid/nucleocapsid
2) contact with special nuclei-acid binding proteins 3) cellular DNA-binding proteins |
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How are papovaviruses packaged?
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Contact with cellular DNA-binding proteins!
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Name 4 routes of entry of viruses:
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-respiratory tract
-alimentary tract -subcutaneously -sexually |
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What percentage of worldwide deaths are caused by infectious disease?
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16%
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Which viruses play a role in the large infectious killers of the world?
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influenza, AIDS, measles...
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Name 3 RNA viruses that enter via the respiratory tract and spread systemically:
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- Measles
-Mumps -Rubella |
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What virus family causes measles and mumps?
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paramyxovirus
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Which of MMR is targetted for world irradication?
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-Measles
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What virus causes Rubella?
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Togaviridae
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What vaccine is good for measles, mumps and rubella?
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MMR
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Name two DNA viruses that enter the respiratory tract and spread systematically:
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-poxvirus
-herpesvirus |
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Which virus was irradicated from the world in 1979?
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smallpox (variola major/minor)
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What disease is caused by a member of orthomixovirus family?
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influenza
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What is the form of the influenza genome?
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8 strands of (-) RNA
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What is the reservoir of influenza A?
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aquatic birds (most virulent)
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What is the reservoir of influenza B?
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humans
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What is the reservoir of influenza C?
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humans and pigs
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What strain of influenza is most fatal?
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H5N1
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What strain of influenza is easily spread?
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H1N1
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What virus family is the cause of SARS?
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coronavirus
(+) RNA |
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Paramyxovirus causes a disease besides measles and mumps. What is it?
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Respiratory syncytial virus
nearly all children infected by age 2-3 treatment = oxygen |
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What kind of viruses play a huge role in developing countries, but not in ones already developed?
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Acute Gastroenteritis Viruses
(diarrheal) |
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Adenovirus can enter the body via the respiratory tract or via the alimentary tract. Which is more severe?
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alimentary tract (spreads sytematically)
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Name 4 RNA viruses that enters via the alimentary tract and spread systematically:
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enterovirus
poliovirus hepatitis A virus reovirus |
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Name a DNA virus that enters via the alimentary tract and spreads systematically:
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adenovirus
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Name 3 RNA viruses that replicate in the intestine
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coronavirus
Norwalk (calici) rotavirus |
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Name 2 DNA viruses that replicate in saliva
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herpes simplex
Epstein-Barr |
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Where does the poliovirus replicate? What does it ultimately cause?
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lower/upper alimentary tract
paralysis (rare) |
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Name some RNA transcutaneous viruses:
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Flaviviruses: hepatitis C, dengue, yellow fever, West Nile
Rhabdovirus: rabies Retrovirus: HIV Ross river virus: Toga |
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Name 2 DNA transcutaneous viruses:
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HPV (papilloma)
HBV (hepadna) |
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Name some DNA viruses that are sexually transmitted:
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HSV2 (herpes)
HBV (hepadna) Papillomavirus |
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What is the origin of HIV virus?
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Simian monkey virus
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Name some treatments for HIV:
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-RT inhibitors (nucleoside/non)
-protease inhibitors -entry inhibitors -integrase inhibitors |
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Which viruses, respectively, cause hepatitis A, B, and C?
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A - picornavirus (acute)
B - hepadnavirus (acute/chronic) C - flavivirus (chronic) |
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Which type of hepatits does not have a vaccine?
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C
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What DNA virus has over 150 varieties, and 8 human members?
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Herpes virus
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What is a drug that treats herpes?
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aciclovir
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Which virus is responsible for cervical cancer?
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HPV
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What virus causes rabies?
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lyssavirus
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What is a symptom of rabies?
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acute encephalitis
fatal |
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How does the rabies virus spread?
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enters PNS and spreads to CNS
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What virus causes Yellow Fever?
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Flavivirus
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How is yellow fever transmitted?
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by mosquito bite
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What type of genome does lyssavirus have?
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(-) strand RNA
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What type of genome does Flavivirus have?
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(+) strand RNA
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What are the 4 stages of viral replication?
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1. Entry
2. Genome replication 3. Gene expression 4. Assembly |
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How does a virus meet up with a cell?
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by random chance, the same as macromolecules
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Which method of entry is generally used by viruses?
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receptor-mediated endocytosis
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Name two criteria for virus entering a given cell:
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1. host range
2. tissue tropism |
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What was the first known virus receptor?
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sialic acid (for influenza, and others)
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What advances in technology allowed for discovery of many viral receptors? (4)
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-monoclonal antibodies
-recombinant DNA techniques -mutagenesis analysis -transgenic mice |
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What is the receptor for rhinovirus?
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Icam-1
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How was the rhinovirus receptor purified?
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monoclonal antibodies
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What are the 4 steps of viral entry?
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1. attachment
2. penetration 3. transport to site of replication 4. uncoating |
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Name 5 different classes of virus receptors:
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IG family
LDL receptor family multi-TM spanning transport proteins integrins specific carbs on glycoproteins/proteoglycans/glycolipids |
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Name 3 viruses whose receptor is sialic acid:
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human coronavirus
influenza A, B, C |
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What are the receptors for HIV-1
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CD4 and CXCR4/CCR5
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Which 2 viruses whose receptor is heparan sulfate?
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HSV-1
Vaccinia virus |
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What is the poliovirus receptor?
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Pvr
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What is the adenovirus receptor?
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Car
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What is the rhinovirus receptor?
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Icam-1
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What is the enterovirus receptor?
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CD55
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What is the echovirus receptor? (1 and 8)
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alpha 2 beta 1 integrin
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Which virus can change receptors?
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Foot-and-mouth disease: alpha 5 beta 2 intergrin to heparan
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How do non-enveloped viruses bind to cell receptors?
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capsid proteins
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How do enveloped viruses bind to cell receptors?
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surface glycoproteins
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Describe the binding of rhinovirus to its receptor.
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D1 domain of Icam-1 binds with the canyon of V1, V2 and V3 proteins
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What are the roles of HA and NA of influenza?
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HA1 binds sialic acid receptor
NA cleaves sialic acid from galactose so virus is not stuck to progenitor cell |
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How do HIV-1 env proteins bind to its receptor and co-receptor?
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Gp120 binds to CD4 inducing a conformational change, so it also binds CCR5
Gp41 is the envelope TM domain |
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Which enveloped viruses uncoat at the PM?
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Sendai
Simian virus 40 simple retro virus HIV-1 |
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Which enveloped virus uncoats within an endosome in the cytoplasm?
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influenza
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What is the mechanism for envelopped virus penetration of cells?
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use of fusion peptide
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Give 2 examples of viruses with two viral surface proteins:
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Sendai virus (1 cell protein)
Simian virus (2 cell proteins) |
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Name 2 viruses with a single viral glycoprotein that serves as a fusion protein:
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simple retrovirus
HIV-1 |
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Which is HIV-1's fusion protein?
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Gp41
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What is characteristic of influenza's fusion to the endosome? (2)
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-pH dependent
-coiled-coil hydrophobic structure in which fusion peptide is hidden until presentation to receptor |
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What virus causes cell lysis?
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adenovirus
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Which virus injects its genome into the cytoplasm?
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poliiovirus
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How does a virus travel through the cytoplasm?
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following microtubule and using dynein motorproteins
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Name a virus whose nucleocapside travels the cytoplasm microtubules:
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HIV-1
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Which intact virus particles can enter the nuclear pore?
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parvovirus
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Which virus particles parially dissemble before entering the nuclear pore?
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herpesvirus
adenovirus |
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Which virus particles enter the nucleus during mitosis?
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simple retroviruses (cannot infect nondividing cells)
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Which step of viral entry is the least well understood?
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uncoating
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Which virus uncoats in the cytoplasm?
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HIV-1
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Which virus uncoats at the face of the nuclear pore?
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herpesvirus
adenovirus |
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Which virus uncoats in the nucleus?
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parvovirus
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Which virus uncoats during entry?
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picornavirus
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Name 6 ways to prevent entry:
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-neutralizing Abs
-soluble/truncated versions of cellular receptors -proteins/Abs that bind receptor -compounds that prevent acidification of endosomes -fusion inhibitors -agents that prevent virus uncoating |
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Name some compounds that prevent acidification of endosomes:
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NH4Cl - lysomotropic agent
Menensin - carboxylic ionophor bafilomycin A |
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What type of genome does influenza have?
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(-) RNA
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What type of genome does hepatitis C have? (flavivirus)
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(+) RNA
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What type of genome does rotavirus have?
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dsRNA
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What type of genome does HIV have?
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(+) RNA
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What type of genome does hepatitis have?
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dsDNA
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What type of genome does parvovirus have?
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ssDNA
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What type of genome does herpesvirus have?
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dsDNA
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Name an example of a virus that has a DNA-dep. DNA-pol.:
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klenow virus
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Name a virus that has a DNA-dep. RNA pol.:
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T7 RNA-P
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Name a virus that has an RNA-dep. RNA pol:
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poliovirus
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Name 2 viruses that have RNA-dep. DNA pol.:
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retroviruses
hepatitis B virus |
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What are features of polymerase proteins? (3)
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-conserved motifs
-similar tertiary struction -right hand with a palm, finger, and thumb |
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Which RNA virus uniquely uses a cellular accessory protein?
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hepatitis delta (needs delta antigen)
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Which accessory proteins does influenza virus need?
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PB1 needs PA, PB2, and NP
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Which 3 RNA viruses exceptionally need primers?
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picornavirus - protein
influenza - capped RNA bunyavirus - capped RNA |
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Name 2 viruses with (-) RNA
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-influenza
-VSV |
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How does VSV control gene expression in a special way?
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Intergenic junctions (Ig) where RNA-pol. falls off RNA
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Name 4 viruses with (+) RNA:
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-Flavivirus
-Alphavirus -Sindbis virus -Picorna virus |
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How does Sindbis virus control translation of its genome?
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sequential cleavage of RNA-pol.
1. (-) RNA 2. (+) RNA and (-) RNA 3. only (+)26X and (+)49S RNA |
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Why does dsRNA never leave the viral capsid?
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to evade Dicer
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What kind of RNA virus can use both (+) and (-) strands as its genome? Give an example:
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ambisense RNA
Arenavirus |
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What are the 3 stages of retrovirus genome replication?
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1. initiation
2. first template exchange 3. second template exchange |
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Which enzymes are useful for retrovirus replication?
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reverse transcriptase
RNAaseH viral integrase |
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How is the DNA of a retrovirus integrated in a host cell chromosome expresses?
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by RNA-pol. II
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Name a retrovirus whose DNA does NOT get integrated into its host cell:
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Hepatitis B virus
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How is the hepatitus B virus replication primed?
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by a protein (viral polymerase peptide) at 5'-end of pre-genomic RNA
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Name 4 exceptions of RNA viruses that replicate their genomes in the nucleus:
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-influenza
-borna disease virus -hepatitis delta virus -retrovirus |
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Are DNA-viruses always primed?
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yes! Even though some can be primed by only DNA e.g. parvovirus, poxvirus
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Which direction does replication go?
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5' --> 3'
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Which 3 viruses use cellular DNA-pol.?
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parvovirus
papovavirus Epstein-Barr ** (Ori-P) |
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Which 3 viruses use viral DNA-pol.?
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adenovirus
herpesvirus ** (Ori-Ly) poxvirus |
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How do cells deal with shortening ends of DNA
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telomerase
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How do DNA viruses deal with shortening ends of DNA?
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circular genomes
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What kind of viral genomes generally use an RNA primer?
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circular DNA
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Give 2 examples of viruses that use RNA primers:
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papovavirus
herpesvirus |
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GIve 2 examples of viruses that use DNA as primer for replication:
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parvovirus: T-structure/panhandle
poxvirus: hairpin model |
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Name a virus that uses a protein primer:
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adenovirus
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Which machinery do viruses use to express their genome?
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cellular machinery
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Which polymerases do RNA viruses use?
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viral RNA-dep. RNA-pol.
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Which polymerases do retroviruses and DNA viruses use?
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DNA-dep. RNA-pol. (mostly cellular, sometimes viral)
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Name a virus with a DNA genome that replicates in the cytoplasm and carries its own enzyme for transcription:
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poxvirus
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What type of RNA viruses must carry their own machinery for transcription?
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(-) ssRNA
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What type of RNA virus carries its genome in particles at ALL times?
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dsRNA
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Which cellular RNA-pols are used by viruses? (DNA/retro)
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RNA-pol. II and occasionally RNA-pol. III
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Where does cellular RNA-pol. bind to transcribe viral DNA?
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the viral genome promoter (TATA sequence)
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Where do viral control factors bind to viral DNA?
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local regulatory sequences/distal regulatory sequences
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What are two ways that TFs can bind to viral DNA?
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sequence-specific/sequence-non-specific
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Explain how transcription is stimulated in HIV-1:
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Tat protein binds to the TAR region, recruiting cellular factors such as CDK9, which hyperphosphorylates RNA pol.
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Name 5 ways a viral primary transcript can be "matured":
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-5' cap
-3' poly(A) tail -editing -splicing -nuclear export |
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Which virus which uses its own enzymes for maturation:
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poxvirus
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In which viruses were the 5' cap and poly(A) tail discovered?
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reovirus
vaccinia virus |
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In which virus was splicing discovered?
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adenovirus
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In which virus were internal ribosome entry sites discovered?
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poliovirus
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Name 6 viruses that are capped by cellular factors:
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-parvovirus
-papomavirus -adenovirus -herpesvirus -retrovirus -hepadnavirus (All DNA viruses except poxvirus) |
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Name 3 viruses that use their own enzymes for capping:
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-alphavirus
-rhabdoirus -reovirus ect... RNA viruses |
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Name 2 viruses that acquire their caps from cellular mRNA:
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-influenza (orthomyxo)
-bunyavirus |
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Name 2 viruses that are NOT capped:
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-picornavirus
-hepatitis C |
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What category of viruses are poly(A)ed during mRNA synthesis?
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RNA
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What category of viruses are poly(A)ed after mRNA synthesis?
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DNA
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Rhabdoviruses, paramixo, orthomixo poly(A) how?
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short U stretches
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Picorna and togavirus poly(A) how?
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long 5'-terminal stretches
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What is editing?
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Adding extra uncoded NTs into the mRNA during or post-transcription
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Give examples of 2 viruses that insert NTs into their primary transcript:
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paramyxovirus
filavirus |
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Hepatitis delta satellite virus edits its primary RNA transcript using this special method:
|
A --> inosine
via dsRNA adenosie deaminase |
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Name 3 viruses that use alternative splicing:
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-Simian virus 40
-Papillomavirus -Retrovirus |
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HIV-1 and Mason-Fizer monkey virus can transport unspliced mRNA from the nucleus -- how?
|
CTE (control transport element) is recognized by proteins for transport.
HIV-1 "Rev" MFMV cellular "UAP55" |
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How is translation modulated in viruses? (6)
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1. IRES
2. Polyprotein synthesis 3. Leaky scanning 4. Reinitiation 5. Suppression of termination 6. Ribosomal frameshift |
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What is IRES?
|
internal ribosome binding
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Name 2 viruses that do IRES:
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-picornavirus
-flavivirus |
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What is polyprotein synthesis?
|
Synthesis of one polypeptide which is cleaved to form many products.
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Name 4 viruses that do polyprotein synthesis:
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-picornavirus
-flavivirus -alphavirus -retrovirus |
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What is leaky scanning?
|
Reinitiation at a second AUG on the mRNA
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Name 5 viruses that do leaky scanning:
|
-Sendai virus
-Influenza B -HIV-1 -Human T-cell leukemia virus -Simian virus 40 |
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Which viruses do reinitiation?
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-influenza B
-CMV |
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Which viruses suppress termination?
|
-alphavirus
-retrovirus |
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Which viruses can do ribosomal frameshifting?
|
-coronavirus
-human astrovirus I -retrovirus |
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Which viruses can form secondary mRNA structure useful for cap-independent initiation of translation? (3)
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-EMCV
-HCV -CrPV (cricket paralysis) -- directly recognized by 4DS ribosome!!! |
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Which virus is a model for the stepwise assembly line of the viral capsid?
|
-T4 bacteriophage
|
|
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Name 2 viruses assembled from individual protein molecules:
|
-Simian virus 40
-adenovirus |
|
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Name a virus assembled from a polyprotein precursor:
|
poliovirus
|
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Which signals are used for packaging by DNA and RNA viruses, respectively?
|
DNA and RNA signals
|
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What are herpesvirus I`s packaging signals?
|
Pac1, Pac2
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What is adenovirus 5`s packaging signal?
|
5` tandem DNA sequences
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What is HIV-1`s packaging signal?
|
stem-loop structur recognized by Gag (nucleocapsid protein)
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Name 2 viruses assembled in the nucleus:
|
-adenovirus
-herpesvirus I |
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Name a virus assembled in the cytoplasm:
|
-poliovirus
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Name 2 viruses assembled at the PM:
|
-influenza virus
-retrovirus |
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What type of maturation does influenza undergo?
|
removal of sialic acid by NA
|
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What maturation does HIV-1 undergo?
|
cleavage of Gag precursor at 5 sites
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How are enveloped viruses released?
|
budding or exocytosis
|
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Hoaw are non-enveloped viruses released?
|
cell lysis
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What does ``maturation`` mean?
|
Modifications for virus particles to become infectious.
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What maturations steps does poliovirus undergo?
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cleavage of N-S dipeptide to release VP2 and VP4 from VP0
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