BOMI 357 Molecular Virology Fall 2016 (Ambegaokar)

Ch. 33 (Acheson) Reading Guide

Intrinsic Cellular Defenses Against Viral Infection

1. What are the typical first lines of defense that multi-cellular organisms use to
prevent infection from pathogens, including viruses?

2. What are the 3 stages of intrinsic cellular defense against pathogens?

3. A) If a pathogen is able to evade intrinsic cellular defense and spread to several

other cells or tissues, what 2 organismal-wide immune responses are
generated?

B) Which of these 2 typically acts more quickly?

4. A) Name 3 cell types associated with the innate immune system.

B) Name 2 cell types associated with the adaptive immune system.

5. A) Where are toll-like receptors (TLRs) typically found in a cell?

B) What are PAMPS (short for pathogen associated molecular patterns)?

C) In what species were TLRs (or just Toll receptors) first discovered?

D) From which type of pathogen did they provide defense in this species?

E) How many different TLRs do humans have? How many do mice have?

6. A) Which TLRs recognize lipoproteins and glycoproteins that are often found in
many enveloped viruses?

B) Where are these TLRs usually found in a cell?

7. A) Which TLRs recognize viral nucleic acids (DNA or RNA)?

B) Where are these TLRs usually found in a cell?

8. A) The presence of what type and structure of nucleic acid is the most reliable
indicator of a virus infection?

B) Which TLR can recognize this indicator?

9. A) Which cell type(s) express TLR-3?

B) Which cell type(s) express TLR-7, -8 and -9?

10. A) What cellular process is induced during period of cellular stress, such as
nutrient starvation or infection?

B) How is this process thought to help viral infection recognition by TLR-7?

11. A) TLR-3 is a membrane-bound receptor that recognizes dsRNA.

Name 2 cytoplasmic receptors that also bind to dsRNA.

B) Which one of these preferentially recognizes short dsRNA molecules?

C) What is the synthetic molecule polyI:C meant to mimic?

12. A) While dsRNA is uncommon in most host cells, and thus is a reliable indicator
of viral infection, host cells also produce proteins that recognize dsDNA which
also initiate an antiviral response. But host cells also contain dsDNA even in
the absence of infection. How does the cell distinguish dsDNA from infection
versus endogenous dsDNA?

B) Name 3 cytoplasmic dsDNA binding molecules, used in pathogenic detection.

13. Besides pro-inflammatory cytokines, what is the major class of cytokines that
are synthesized and/or secreted in response to PAMP-binding to TLRs or
cytoplasmic pathogen receptors?

14. When cellular detector proteins recognize viral components, they initiate
___________ _____________ ___________ that activate a variety of __________________
______________, which in turn activation transcription of many cellular
_______________ ___________.

15. A) When TLR-3 is activated, to which adaptor protein does it bind to initiate a
signal transduction pathway?

B) When other TLRs are activated (not TLR-3), to which adaptor protein do
they bind to initiate a signal transduction pathway?

C) Which TLR can interact with both types of adaptor proteins?

 D) When RIG-1 or MDA-5 are activated, to which adaptor protein do they bind to
initiate a signal transduction pathway?

16. A) Name 2 kinases that are activated by either TRIF, MyD88 or IPS-1.

B) Name 3 transcription factors that become active (translocate from the

cytoplasm to the nucleus) due to activation of the 2 kinases listed in (A).

C) What types of genes are turned on when these transcription factors

translocate to the nucleus?

17. A) What are cytokines and what is their function?

B) What are the 4 major classes of cytokines?

C) IL-1, IL-6, IL-12, and TNF- are examples of which class of cytokine?

D) IL-4, IL-10, and TGF- are examples of which class of cytokine?

E) IL-8, CXCL10 and RANTES are examples of which class of cytokine?

18. If pro-inflammatory cytokines are needed to ward of

infection, what is the purpose of anti-inflammatory cytokines?

19. A) What is apoptosis?

B) Why can apoptosis be an effective host defense system to infection?

20. A) The regulation of apoptosis is carefully controlled though signal transduction

pathways. What is the final class of proteins that are activated to directly
cause cell death?

B) Why arent these proteins active all the time?

C) At which amino acids do most caspases cleave (full name, 1-letter and 3-letter
abbreviations).

21. Cytochrome c is the major trigger for apoptosis in the intrinsic pathway of
apoptosis signaling. From were does cytochrome c come, and where does it go?
22. A) What is the function of the inflammasome?

B) Which caspase is activated in inflammasomes?

C) Which cytoplasmic sensors lead to the activation of this caspase?

23. A) Which cytokines possess the strongest antiviral activity, specifically?

B) How many classes of interferons are there?

C) Interferons & are classified under which class of interferon?

D) Interferon is classified under which class of interferon?

E) ) Interferons 1, 2, and 3 are classified under which class of interferon?

24. Besides antiviral effects, what other functions do interferons have?

25. A) Recombinant interferons & are used to treat which types of infections or
diseases?

B) What are the limitations in using recombinant interferon as a therapeutic

intervention for diseases?

26. T lymphocytes and NK cells primarily produce which type of interferon?

27. Transcription factors such as IRF-3, IRF-7, NF-B, and ATF-2/c-Jun induce
transcription of interferon classes I & III. What is the name of the regulatory
region of DNA to which they bind, that is hundreds of nucleotides upstream of
the transcription start sites for IFN-I and -III genes?

28. A) How many transcription factors of the IRF family are presently known?

B) In addition to activating interferon genes, with what other biological

processes are these transcription factors involved?

29. A) Interferons are secreted into the extracellular environment to be detected by

neighboring cells (or distant cells via the circulatory system). What type of
receptor is usually needed to bind to secreted (extracellular) interferons?

B) Activation of these receptors usually activates what type of transcription

factor?
30. A) Which receptors bind to IFN- and IFN-?

B) Which receptors bind to IFN-?

31. A) Although IFNAR1 and IFNAR2c are expressed in nearly all cell types, which
cell type is the only one that expresses IL28R?

B) To which type of interferon does IL28R bind?

C) What is one theory as to why only these cell types express this particular
interferon receptor (IL28R)?

32. A) What class of genes are induced by Stat1/Stat2/IRF-9?

B) How many such genes have been identified?

33. A) Mx proteins are most effective at inhibiting which types of viruses:

RNA or DNA?

B) What aspect of viral replication do Mx proteins inhibit?

C) Why would the sub-cellular localization of Mx1 protein help in limiting

influenza virus, but not rhabdoviruses?

34. A) Ribonuclease L is a potent enzyme that can degrade viral mRNAs, but also
host mRNAs and so is normally kept inactive. What product leads to the
activation of ribonuclease L?

B) What enzyme leads to the production of this product?

C) How is this enzyme activated?

35. T/F: Ribonuclease L and 2, 5 oligo(A) synthetase are both considered as ISGs.

36. Name 2 interferon stimulated genes (ISGs) that are enzymes that become active
when they bind to dsRNA.

37. A) Activated PKR phosphorylates eIF-2 at which amino acid?

B) When eIF-2 is phosphorylated at this amino acid, how is this an antiviral

response?
 C) This amino acid can be phosphorylated because it has a hydroxyl group.
Which other amino acids, then, can also become phosphorylated?

D) p53 and PKR are both involved in inducing ___________________.

38. Name 3 viral products (from any viruses) that inhibit PKR function.

39. What are v-IRFs and what is their function?

40. Which virus produces proteins CrmA, CrmB, and CrmC, and what are their
functions?

41. A) Only mammals produce interferons. What do plants, invertebrates and fungi
use instead as potent anti-viral defenses?

B) What is the major enzyme required to initiate this mechanism?

42. What are RISC complexes?

43. T/F: Argonaute proteins are part of RISC complexes.

44. T/F: Mammals express both interferons and RNAi mechanisms.