Topic 4

Question 1

What is the main special attribute of retroviruses?

Answer 1

They are able to insert their genomes into the host cell’s chromosomes (and thus be passed on to cell progeny)

Question 2

How many genera of retroviruses are there?

Answer 2

7

Question 3

What is the classification of retroviruses based of?

Answer 3

Pathogenicity
Nucleotide sequence
Genome structures

Question 4

What generus does HIV belong in?

Answer 4

Lentiviruses

Question 5

What does HIV stand for?

Answer 5

Human Immunodeficiency virus (HIV)

Question 6

What disease does HIV cause?

Answer 6

Acquired ImmunoDeficiency Syndrome, or AIDS

Question 7

What is AIDS characterized by?

Answer 7

Susceptibility to opportunistic pathogens
Kaposi’s sarcoma
B cell lympohoma
Profound loss of CD4+ T cells

Question 8

What is the differences between HIV-1 and HIV-2?

Answer 8

HIV-1 and HIV-2 has a smilar mode of transmission, but NF-|B needs to be present.

Average time from infection to disease progression is longer in HIV-2 infected individuals

Question 9

What are unique features of the retrovirus genome?

Answer 9

1. Genome is diploid (2x identical ssRNA)
2. Synthesized & processed by host cell mRNA after virus has integrated DNA into the host cell chromosome
3. Associated with a specific tRNA (from host cell) used to prime replication
4. +-strand RNA with 5’cap and 3’ Poly-A tail but does NOT serve as mRNA immediately after infection

Question 10

What is the invariant gene order in retroviruses?

Answer 10

5’ - gag - pol - env - 3’

Question 11

What is the difference between complex and simple retroviruses?

Answer 11

Complex retroviruses contain additional genes that are involved with gene regulation, whereas simple retroviruses lack those genes.

Question 12

What is the generalized structure of retroviruses (enveloped/not enveloped, capsid structure, etc.) ?

Answer 12

Enveloped
~110nm diameter
Nucleocapsid
Contains Reverse transcriptase and integrase
Conical to spherical capsid shape

Question 13

What is the name of the glycoprotein on the retrovirus surface? What does it do?

Answer 13

• Derived from gp160 (env gene product).
• Has 2 components, surface protein (gp120) and trans-membrane protein (gp41), connected by a disuphide bond
• gp120 binds to CD4 and chemokine receptor (involved in receptor binding)
• gp41 anchors gp120 to the viral envelope and helps in the fusion of the virus with the membrane
  (involved in membrane fusion)

Question 14

What are the products of the gag gene?

Answer 14

Structural proteins (activated by proteolytic cleavage)

• Capsid proteins
• Nucleocapsid proteins (covering RNA)
• Matrix protein (p17)
• Protease (activated when budding out from cell)

Question 15

What are products of the pol gene?

Answer 15

Enzymes required for genome replication

• Reverse transcriptase
• Integrase
• Also activated by proteolytic cleavage

Question 16

What are the products of the env gene?

Answer 16

Envelope proteins for host-cell binding

• gp160 (→ gp120 & gp41 after cleavage by cellular protease)
• gp120 is a surface glycoprotein, involved in receptor binding
• gp41 - involved in membrane fusion (transmembrane protein)

Question 17

What is the host range of HIV?

Answer 17

HIV-1 binds to CD4 on T helper cells and some macrophages, using either CCR5 or CXCR4 co-receptors.
Infects

Question 18

How is HIV transmitted?

Answer 18

Through direct contact of a mucous membrane or bloodstream with a biological fluid containing HIV-1 (blood, semen, vaginal fluid, pre-ejaculate fluid, breast milk)

Question 19

What cells does HIV-1 infect?

Answer 19

CD4 T cells (I.e helper T cells) and macrophages (primarily) but can also infect microglia cells in the brain

Question 20

What happens when chimpanzees get infected with HIV-1?

Answer 20

They develop viremia and antibodies to HIV-1, but HIV-1 is not pathogenic to chimpanzees (so no opportunistic infections, cancers, or decline in CD4 T cells that is seen in AIDS)

Question 21

What is the first step of HIV replication?

Answer 21

Virus attaches to CD4 with glycoprotein gp120, inducing a confirmation change in gp120

• new gp120 confirmation reveals chemokine receptor binding site for CXCR4/CCR5.
• One of the two (CXCR4 or CCR5) binds to the virus, causing a confirmation change in gp41, causing it to insert itself into the host cell membrane, inducing fusion of the virus

Question 22

What is the second step of HIV replication?

Answer 22

Viral vapsid released into cytoplasm, along with the rest of its contents (i.e. Reverse transcriptase, integrase, ssRNA)

Question 23

What happens in step 3 of HIV replication?

Answer 23

RNA genome is reverse transcribed by reverse transcriptase into double-stranded DNA, producing the provirus DNA intermediate

Question 24

What are the three main enzymatic activities of reverse transcriptase?

Answer 24

RNA dependent DNA polymerase
RNase (degrades RNA)
DNA dependent DNA polymerase

Question 25

What is special about reverse transcriptase and retroviruses?

Answer 25

It is unique to retroviruses

Question 26

How does reverse transcriptase (RT) create DNA from RNA in HIV?

Answer 26

-tRNA binds to a complementary sequence on (+) strand - RT uses the tRNA as a primer to synthesize the complementary (-) DNA strand using RNA-dependent DNA polymerase activity (RDDP) - RNase H activitity of RT removes 5' end of viral RNA - Remaining short DNA fragment can bind to the 3' end of the other RNA strand, allowing RDDP activity of RT to replicate the remainder of the DNA strand - RNase H activity of RT removes most of RNA strand to create primers for DNA synthesis - RNA primer formed by RNase H activity is used to synthesize the (+) sense DNA strand, using the (-) sense DNA strand as a template - dsDNA has been created from the ssRNA