Ch. 7 Reverse Transcription and Integration

Question 1

Where does the name retrovirus come from?

Answer 1

The retrograde flow of information

Question 2

Reverse Transcriptase needs a ______ to initiate DNA synthesis.

Answer 2

specific primer

Question 3

Retroviral particles contain ___ copies of the genome. This complex also includes two molecules of ____. What is their purpose?

Answer 3

two; they are held together by multiple regions of base pairing at the 5’ end sequences. tRNA. They serve as a primer.

Question 4

Where does the tRNA bind?

Answer 4

the primer binding site (pbs) near the 5’ end of the RNA genome.

Question 5

What are the activities of RT?

Answer 5

RNA dep. and DNA dep. DNA synthesis; DNA unwinding; hydrolysis of RNA in RNA-DNA hybrid by RNase H.

Question 6

What is the purpose of RNAse H?

Answer 6

It degrades genomic RNA template strand after DNA comp. strand has been synthesized.

Question 7

How is the (-) strand of DNA initiated? What is the initiation piece of DNA called?

Answer 7

Retroviral transcription starts near the 5’ end of the genome. This small segment of DNA is synthesized from RNA template, and then corresponding RNA is degraded;
(-) Strong Stop DNA

Question 8

Complementary pieces of (-)strong stop DNA and 3’ end of genomic RNA engage. This is called:

Answer 8

The first template exchange

Question 9

DNA is then synthesized all the way to the 5’ end of the template strand. RNase digests the RNA template strand, leaving chunks of RNA called:
What do these act as? What is the name of the resulting DNA?

Answer 9

Polypurine tracts. These act as primers
(+) Strong Stop DNA results, and the DNA template exchange occurs to allow synthesis of remaining (+) strand DNA. (+) Strong Stop DNA

Question 10

The final product is:

Answer 10

A linear DNA duplex copy of the viral genome.

Question 11

RT is encoded by:

Answer 11

pol genes.

Question 12

What is the class of protein for RT?

Answer 12

a heterodimer. Only one subunit has RNase H activity.

Question 13

What is the speed of RT?

Answer 13

SLOW…. 1-1.5 nucleotides/second. 10X slower than DNA dep. DNA pol. It takes HIV 4 hours to copy its genome after infection.

Question 14

Where does DNA synthesis take place?

Answer 14

The cytoplasm, in a subviral complex called an RT complex.

Question 15

What would be a good target for fighting AIDS?

Answer 15

Reverse transcriptase; also integrase

Question 16

Subunits of RT dimer are structurally:

Answer 16

asymmetric.

Question 17

How many Reverse Transcriptases are typically present in a retroviral particle (virion)

Answer 17

50-100 copies.

Question 18

Why is there a high rate of mutation in retroviruses?

Answer 18

Lack of proofreading. 1 error per 10^4 nucleotides. For HIV this means one lesion per genome per cycle.

Question 19

What allows for insertion of DNA product into host DNA? What is the name for this new viral DNA?

Answer 19

integrase (IN);

Proviral DNA

Question 20

Where is Integrase encoded?

Answer 20

the 3’ End of the RT pol gene. It is produced by viral protease processing of Gag-Pol

Question 21

When integrated, how many base pairs of the virus are cropped? What happens to the host DNA?
What is also present?

Answer 21

2 from each side. ;
There is a short duplication so host DNA is the same on both sides of proviral DNA;
Short, inverted repeats at the termini

Question 22

What is the structure of Integrase?

Answer 22

It exists in monomeric, dimeric and tetrameric forms in absence of DNA substrate. The tetramer is stabilized by interaction with a pair of DNA ends

Question 23

How does integrase work?

Answer 23

Nicking of host DNA and then addition of viral DNA. Host senses damage and “repairs” DNA