Viral structure and replication I&II-Saviola

Question 1

What are the basic properties of viruses?

Answer 1

Do not: generate metabolic energy or perform protein synthesis.
Are not susceptible to antibiotics.
Reproduction involves host cell synthesis of subunits then assembly into viron

Question 2

What is a virion?

Answer 2

the mature infectious virus particle.

Question 3

What is a capsid?

Answer 3

the protein shell that encloses and protects the viral nucleic acid.

Question 4

What is a nucleocapsid?

Answer 4

the internal part of the virus particle, which consists of the nucleic acid and closely associated proteins, used when this complex is a discrete substructure of a complex particle.

Question 5

What is the envelope?

Answer 5

the viral membrane, consisting of a lipid bilayer, proteins, and glycoproteins.

Question 6

What is +ssRNA?

Answer 6

single stranded RNA of the same polarity as mRNA.

Question 7

What is -ssRNA?

Answer 7

single stranded RNA complementary to mRNA.

Question 8

What is DNA dependent RNA polymerase?

Answer 8

an enzyme that uses DNA as a template for producing RNA (your cells use this to transcribe genes).

Question 9

What is RNA dependent RNA polymerase?

Answer 9

an enzyme that uses RNA as a template for producing RNA (viruses use this to make mRNA and RNA genomes, not present in host).

Question 10

What is DNA dependent DNA polymerase?

Answer 10

an enzyme that uses DNA as the template for producing DNA (your cells use this to replicate).

Question 11

What is RNA dependent DNA polymerase?

Answer 11

an enzyme that uses RNA as the template for producing DNA (reverse transcriptase in retroviruses and HepB, not present in host).

Question 12

What is cDNA?

Answer 12

complementary DNA made from RNA by recombinant procedures. It can be cloned and used for many purposes. In virus made by reverse transcriptase.

Question 13

What is Transfection?

Answer 13

infection of mammalian cells by bare viral nucleic acid.

Question 14

What is Transformation (in virology)?

Answer 14

a stable heritable change in the genetic makeup and phenotype of a cell resulting from the infection of that cell by a virus. (Usually implies converting to a neoplastic phenotype.)

Question 15

What are Permissive cells?

Answer 15

cells that support the complete virus life cycle, with production of infectious virus particles.

Question 16

What are Nonpermissive cells?

Answer 16

cells which permit none of or only part of the virus life cycle. Often nonpermissive cells are transformed by viruses. Applies especially to DNA viruses.

Question 17

What is a Defective virus:

Answer 17

a virus that is not capable of going through its entire replication cycle unless the cell is infected with a complete virus (helper) particle as well.

Question 18

What is Cytopathic effect (CPE)?

Answer 18

observable damage to a cell resulting from virus infection.

Question 19

What is the structure of animal viruses?

Answer 19

Tiny (can’t see with light microscope)
Nucleic acid = genetic material
-Variable amount (codes for 3-100s of proteins)
-Genome can be segmented or single piece.
-Can be DNA or RNA but not both.

Question 20

What is the structure of a capsid?

Answer 20

Formed of protein subunits called structural units or capsomers.
Protects the enclosed nucleic acid.
Topology:
1. Complex- found in poxviruses; their morphology is different from that of other viruses. (least common)
2. Icosahedral- Solid w/ 20 triangular faces, 12 vertices, 2, 3, 5 fold symmetry. (almost spherical)
•Can be naked or associated w/ an envelope.
3. Helical- helical morphology.
•Always has an envelope associated with them.

Question 21

What is the structure of the envelope?

Answer 21

oSurrounds the nucleocapsid.
oFormed from modified host cellular membrane.
oContains host derived phospholipid bilayer.
oContains virus-derived proteins and glycoproteins-for attachment and viral fusion.
oMatrix proteins (M proteins) are often found associated with the inner layer of the envelope. Aid in viral structure.
oFusion proteins (F proteins) are found on the envelope surface, they cause viral membranes to fuse with cellular membranes.
oMembranes on enveloped viruses are essential for their functioning. These types of viruses cannot function without that lipid component. Membranes are much easier to strip away with detergents (soap) than proteins and so are much more susceptible to inactivation than unenveloped viruses.

Question 22

How are viruses classified?

Answer 22

6 DNA and 13 RNA virus families in humans based on:
•Chemical nature of nucleic acids.
•Symmetry of nucleocapsid.
•Presence of an envelope 
•Dimensions of the virion and capsid
•nucleic acid sequence similarities

Question 23

Steps of viral infection: Describe 1. attachment.

Answer 23

1. Attachment to host cell
   Virus needs viral receptors on the host cell. (most important factor)
   •This leads to specificity to some hosts or even tissues w/n host.
   •Examples: HIV-1
   oUses the CD4 receptor present on macrophages and T-cells. (normally binds to MHC class II for T-cell response)
   oNeeds coreceptors, Cxcr4 and Ccr5 which are normally chemokine receptors on immune cells.
   oHIV proteins SU and TM (fusion peptide) bind to CD4 and coreceptors.

Question 24

Steps of viral infection: Describe 2. entry into host cell. 3. Synthesis of viral proteins and genome.

Answer 24

2. Entry into host cell
   Different methods of getting in depending on viral family.
3. Non-enveloped viruses:
   oBind to host cell at surface and rearrangement of capsid protein.
   oViruses engulfed by receptor mediated endocytosis. There is partial breakup of the capsid in the vacuole, followed by migration into the cytoplasm for further uncoating.
4. Enveloped viruses:
   oFusion of viral membrane and cell membrane mediated by a viral F protein (fusion protein).
   •No F protein = no fusion.
   oPhagocytosis and fusion of viral membrane with membrane of phagosome mediated by a viral F protein.

Question 25

How does poliovirus enter host cell?

Answer 25

Example: poliovirus

•Binds to receptors → conformational change of VP1 → pore forms → genomic material comes in.

Question 26

How does adenovirus enter host cell?

Answer 26

Example: adenovirus
•Penton base interacts w/ integrin receptor → endocytosis → disassembly of pentons → penetration of capsi to cytoplasm → docking of capsid to nuclear pore → viral DNA goes into nucleus.
•Growth curve:
oEclipse period: no infectious particle
oLatent period: no extracellular virus detected.

Question 27

How does influenza enter host cell?

Answer 27

Example: influenza
•Hemmaglutinin binds sialic acid containing receptors → endocytosis → lower pH → conformational change → fusion of peptides into endosomal membrane → released.

Question 28

How does Seliki forest virus enter host cell?

Answer 28

Example: Seliki forest virus
•clathrin-dependent receptor-mediated endocytosis, membrane fusion catalyzed upon acidification, viral RNA tranlocated to cytoplasm, ribosomes initiate translation

Question 29

What is the F Protein?

Answer 29

oFusion protein found in viral envelopes.
oMandatory for viral entry into host cells.
oHas a hydrophobic domain that can insert into the host cell membrane.
oThe viral and host cell membrane are brought into juxtaposition and are ready to fuse.
oThey also promote syncytium formation (giant cell formation). Multi-nucleated cell.

Question 30

What are the DNA virus rules?

Answer 30

1. In DNA viruses the synthesis of virus-coded macromolecules proceeds with synthesis of early proteins (enzymes required for nucleic acid replication) followed by viral genome synthesis, followed by late protein synthesis (structural proteins).
2. In cells infected with DNA viruses, synthesis of viral mRNA must precede protein synthesis.
3. Most DNA viruses depend on the cellular RNA polymerase II, the enzyme that produces cellular mRNA.
4. Most DNA viruses replicate in the nucleus.
5. Retroviruses are RNA viruses, but their genomes are reverse transcribed into DNA and RNA pol II produces mRNA.
6. Hepatitis B virus also a DNA virus uses reverse transcriptase in its life cycle.
   •Exception to the rule.
7. Poxviruses are transcribed by viral DNA dependent RNA polymerase and viral accessory proteins because they replicate in the cytoplasm. This process is an exception.
8. DNA viruses use cellular or viral DNA polymerases to replicate their genomes.

Question 31

What are the RNA virus rules?

Answer 31

1. +SSRNA acts like mRNA so if it gets into the host cell, this alone can initiate viral replication and growth.
2. RNA viruses may be unimolecular, segmented, single stranded double stranded, or circular.
3. The synthesis of viral proteins requires viral messenger RNA and host machinery, so if the genetic material of the virus is not +ssRNA, enzymes must be available from the virion to produce +ssRNA from the viral genetic material
4. -ssRNA and dsRNA viruses carry enzymes (RNA dependent RNA polymerase) in their virions to produce +ssRNA to be translated by cellular machinery. Naked -ssRNA and dsRNA are therefore non-infectious.
5. All RNA viruses, except retroviruses, encode an RNA-dependent RNA polymerase to catalyze synthesis of new genomes and mRNA.
6. +ssRNA viruses do not carry a viral RNA polymerase in the viral particle. Protein translated from +ssRNA to produce enzymes: therefore +ssRNA alone is infectious.
7. David Baltimore- retroviruses have RNA directed DNA polymerase (reverse transcriptase RT): makes double stranded DNA to insert into the genome of the cell. Viruses have 50-100 molecules of RT in their capsid. Hepadna viruses (DNA virus) also have RT.
8. RNA dependent RNA polymerase shows a high mutation frequency, partly because of a lack of a proofreading function that assures fidelity in other processes such as DNA replication. (DNA rate is as low as 10-8 to 10-11/nucleotide; RNA rate is between 10-3 and 10-4/nucleotide.) RNA dependent RNA polymerase (reverse transcriptase) may be even more error prone.
9. mRNA and genome synthesis can occur in cytoplasm or nucleus. But generally in the cytoplasm. For some viruses such as influenza mRNA synthesis occurs in the nucleus.
10. RNA viruses have more heterogeneity in the order of their genes transcribed and proteins produced.
11. Segmented genomes can reassert or “shuffle” in an infected host cell.
12. Assembly of structural units of virion protein shells: can be from individual polypeptides, polyprotein precurser, and/or be chaperone mediated
13. Viral proteins such as enzymes and glycoproteins may be sythesized as polyproteins. Some viruses use proteases to cleave polyproteins in to discrete functional viral proteins.

Question 32

Describe the assembly and release of viruses.

Answer 32

oDisintegration of infected cell (burst): especially in the case of naked nucleocapsids.
oSlow release: with acquisition of the envelope as the nucleocapsid buds through a virus modified cellular membranes. Hepatitis B virus does this.
•Budding doesn’t harm the host so you can have cells maintained for many generations w/ budding viruses coming out.