Foundations 2 Week 2-2

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blake
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Foundations 2 Week 2-2
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2013-09-29 08:25:17
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Foundations 2 Week 2-2
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  1. How does the type of viral genetic material affect the replication process?
    • Positive strand RNA viruses can be translated immediately, but sometimes use reverse transcriptase to produce DNA.
    • Negative strand RNA requires a polymerase to  be included in the virus.
    • DNA viruses must first be transcribed.
  2. What are the two major types of viron structures?
    • Icosahedral: May be naked or enveloped
    • Helix: Always enveloped (all infectious helical viruses have an envelope)
  3. Describe the major steps in virus replication.
    • 1) Attachment: Viral surface proteins interact with cell surface receptors. This is why a virus may only affect certain animals, organs, or cells - the cell surface receptors are different.
    • 2) Penetration: This can occur through fusion with the cell membrane (occurs at neutral pH), endocytosis and fusion with the endosomal membrane (low pH), or endocytosis and endosome rupture (uncoating takes place separately in this case)
    • 3) Uncoating: Often occurs as part of penetration.
    • 4) Synthesis, translation, genome replication: Positive sense RNA is ready to go immediately, but can also be incorporated using reverse transcriptase. Negative sense RNA requires a polymerase to be included in the virus.
    • 5) Assembly: The new viruses are assembled.
    • 6) Release: Can be through budding or lysis
  4. Identify all the mechanisms by which viruses spread from person to person.
    • Contact: Direct (touching, kissing), droplets, vertical (transplacental, or during birth), vectors (mosquitoes, mice, etc).
    • Indirect (vehicles): Fomites (inanimate objects capable of harboring a virus, like door knobs), air, and food/water/biological products.
  5. Compare and contrast lytic and latent cycles of viral infection.Lysis: Cell breaks open releasing viruses.Latent:
    • Lysis: Cell breaks open releasing viruses.
    • Latent: aka, lysogenic cycle, the virus may remain dormant for awhile or produce and release viruses slowly, without killing the cell.
  6. What virus causes small pox?
    The variola virus.
  7. What is tropism?
    • Tropism refers to the way in which different viruses have evolved to preferentially target specific host species, or specific cell types within those species.
    • Tropism is determined by cell surface markers and the attachment proteins of the virus
  8. How does MHC restriction work?
    A T cell will only recognize an antigen when bound to the correct type of HLA protein!  Even if the antigen is the same, a TCR won't recognize it on a HLA-B if the TCR is designed for HLA-A, and so on.
  9. Which cells do MHC class I and MHC class II present to?
    • MHC class II cells present to CD4 helper T cells.
    • MHC class I cells present to CD8 T cells.
    • NK cells are activated by a lack of MHC class I.
  10. What are the different isotypes?
    • IgG
    • IgA
    • IgM
    • IgE
    • IgD
    • (those antigens have been "GAMED"!)
  11. Describe the significance of IgG
    • IgG is the most abundant isotype, and the main antibody in the secondary (delayed) response.
    • It crosses the placenta to contribute to fetal immunity.
    • It activates the classical complement pathway, opsonizes bacteria, and neutralizes bacterial toxins and viruses.
  12. Describe the significance of IgA
    • IgA is present in mucosal surfaces and secretions, including breast milk, where it presents bacterial and viral attachment or provides immunity to offspring.
    • It does not fix complement.
  13. Describe the significance of IgM
    • IgM is the first type made by the b cell, and the first one secreted during a primary immune response.
    • It also activates the classical complement pathway, but cannot cross the placenta.
  14. Describe the significance of IgE
    • IgE binds mast cells and basophils, cross-linking when exposed to an antigen to trigger histamine release.
    • IgE plays a large role in allergic reactions and parasitic infections.  
    • Activates eosinophils when worms are present.
    • It has the lowest serum concentrations.
  15. Describe the significance of IgD
    IgD is found on the B cell surface and serum, its function is unknown.
  16. What isotypes do mature B cells express?
    IgM and IgD  (Mature B cells are like doctors, they have an MD)
  17. What isotypes do plasma cells secrete?
    IgA, IgG, IgE (plasma cells are made from B cells, so they are older. They have AGE)
  18. Describe the steps HIV uses to enter a cell.
    • 1) GP120 binds to CD4 receptors on CD4 helper T cells. (Dendritic cells can present HIV virus to CD4 helper T cells)
    • 2) The binding of gp120 to CD4 exposes gp120 chemokine binding domains, which bind CCR5 or CXCR4 on the T cell surface.
    • 3) Binding of the coreceptor exposes gp41, which inserts into the cell membrane and then folds to bring the HIV virus to the cell.
    • 4) The lipid bilayer of the HIV fuses with the lipid bilayer of the cell, bringing the HIV capsid in.
  19. What do you call viruses using CXCR4 or CCR5?
    • Viruses using CXCR4 are called lymphotropic. (4 -> L.  Think, “animals have 4 Legs”).
    • Viruses using CCR5 are called macrophage tropic. (think “big MACs have 5 layers”)
  20. What is Seroconversion?
    • Seroconversion is the point where antigen-specific antibodies begin to be made.
    • For HIV patients, this marks the beginning of the asymptomatic phase.
  21. How is HIV/AIDS diagnosed?
    • A very sensitive HIV-EIA test (ELISA, or Enzyme ImmunoAssay) is performed, providing many false positives.
    • A positive test must then be confirmed (typically by a western blot test, which checks for electrophoresed HIV proteins using specific antibodies).
    • CD4 cell count is the most useful test to determine HIV’s status. CD4 < 200 = AIDS.
  22. What genes do simple and complex retroviruses both share?
    • GAG gene: Produces structural proteins like the capsid.
    • PRO gene: Produces the enzyme protease.
    • POL gene: Produces RT and integrase. Some authors include the PRO gene in the POL gene.
    • ENV gene: produces glycoproteins that are inserted into the lipid bilayered envelope.
    • LTR (long terminal repeat) sequences on both ends of the RNA: Transcription initiation, promoter, and transcription termination sequences.
  23. What genes do complex retroviruses have than simple retroviruses lack?
    Complex viruses also have regulatory and accessory genes that produce spliced mRNA.
  24. What is a provirus?
    A retrovirus that is inserted into the host genome.
  25. What is an Endogenous Retrovirus?
    A retrovirus that is inserted into the germline and transmitted to offspring through the sperm and ova.
  26. What are Oncoviruses?
    • AKA transforming retroviruses - these alter the cell’s growth without killing them. They can immortalize cells by preventing them from completing the cell cycle.
    • They can include onc genes, which cause cancer.
    • Includes HTLV-I and HTLV-II, which posses no onc gene, but change PAT genes, affecting virus replication.
  27. What are Lentiviruses?
    • AKA non-transforming, cytopathic retroviruses
    • These kill cells and cause viremia
    • They do not immortalize cells.
    • Includes HIV and HIV-2
    • Includes lentiviruses.
  28. Describe how HIV replicates
    • 1) After entering the cell, the capsid breaks up, releasing integrase, protease, RT, and double stranded RNA.
    • 2) RT (ribonuclease H and polymerase) goes to work. The ribonuclease H site breaks the RNA into a single strand so the polymerase can add a DNA strand to the RNA. Ribonuclease H then removes the RNA strand so polymerase can create a double stranded RNA.
    • 3) Integrase cleaves a dinucleotide from each side of the DNA and then inserts it into the host DNA.
    • 4) Normal cell transcription produces viral RNA, causing new viruses proteins to be translated.
    • 5) The protease then cleaves the viral protein into 3 smaller proteins that are used to create the virus.
    • 6) The virus then leaves the cell.
  29. At what point is a patient considered to have AIDS?
    • When the CD4 T cell count is less than 200.
    • The normal value is around 1,000.
  30. Describe the process of positive-selection.
    • Positive selection retains T cells that recognize self MHC.
    • It occurs in the cortex, where an MHC molecules will be presented.
    • If the T cell can recognize the cortex, it receives a signal to survive. Otherwise apoptosis occurs.
    • Only about 2% of double positive thymocytes will survive and proceed to negative-selection.
    • If the T cell recognized a MHC class I protein, it downregulates CD4 and becomes a CD8+ T cell.
    • If the T cell recognized a MHC class II protein, it downregulates CD8 and becomes a CD4+ T cell.
  31. What happens if an individual lacks either class of MHC proteins?
    • If an individual lacks MHC class I proteins, CD8+ T cells won't be created during positive-selection.
    • If an individual lacks MHC class II proteins, CD4+ T cells won't be created during positive-selection.
    • Either situation results in Bare Lymphocyte Syndrome.
  32. Describe the process of negative selection
    • Negative Selection deletes self-reactive T cells.
    • It occurs in the corticomedullary cortex where dendritic cells and macrophages present self-peptides to see if the T cells will bind tightly.
  33. What is aire?
    Aire, AKA autoimmune regulator, is a transcription factor expressed in the thymus that causes the thymus to create proteins found all over the body (eg, brain proteins, muscle proteins, etc).
  34. What happens if there is a mutation in the aire gene?
    A mutation in the aire gene will cause Autoimmune Polyendocrinopathy-Candidiasis-Ectodermal Dystrophy, causing T cells that recognize body proteins as pathogens.
  35. What does reverse transcriptase do?
    RT takes a positive sense strand RNA and composes double stranded linear DNA which can be integrated into host DNA.
  36. What is produced from the HIV pol gene?
    • Includes 3 enzymes  - all drug targets               
    • 1) Reverse transcriptase (RT): site of
    • activity for nucleoside analogue anti-retroviral drugs.     
    • 2) Protease: cleaves the polyprotein made
    • from the gag and pol genes, it is site of activity for protease inhibitor
    • anti-HIV drugs             
    • 3) Integrase: integrates viral DNA into
    • host cell, site of activity for integrase inhibitor anti-retroviral drugs
  37. What are the 5 main types of HIV drugs?
    • 1) Reverse Transcriptase (RT) Inhibitors
    • 2) Protease Inhibitors (PI)
    • 3) Integrase inhibitors
    • 4) Attachment inhibitors
    • 5) Fusion inhibitors
  38. What is the rate of error for RT?
    1 to 5 per 10,000 bp (1 bp every 3,000-4,000 bp)

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