Midterm 2 - Notes 1 (Part 2)

Question 1

What did the predecessor acquire? (2)

Answer 1

1. Reverse transcriptase

2. RnaseH

Question 2

RT

Answer 2

Reverse transcriptase

Question 3

RH

Answer 3

RnaseH

Question 4

What are RT and RH?

Answer 4

They are types of enzymes

Question 5

What do LTR retrotransposons acquire? (2)

Answer 5

1. LTRs
2. A protease

• processes primary protein to RT and RH

Question 6

What do retroviruses acquire?

Answer 6

Envelope proteins

- allowing them to leave the cell

Question 7

What do non-LTR retrotransposons gain and allow?

Answer 7

Envelope proteins that allow to encapsulate the complex with the proteins and RNAs

Question 8

What are LINEs?

Answer 8

Non-LTR retrotransposons

Question 9

What can non-LTR retrotransposons do?

Answer 9

They can leave the cell and form viral particles

Question 10

How do retroviruses move?

Answer 10

They move from cell to cell

Question 11

How do retro-transposons move?

Answer 11

Within the cell

Question 12

What do LTR-transposon and retroviruses share?

Answer 12

Mechanism of movement and amplification

Question 13

What are RNA and proteins made by in the lifecycle of retroviruses and LTR transposons?

Answer 13

Regular cellular transcription/translation machinery

• RNA transferase
• can use DNA as a template

Question 14

What kind of proteins do viruses only have?

Answer 14

Enveloped proteins

Question 15

What do enveloped proteins allow?

Answer 15

Movement from cell to cell

Question 16

What do retrotransposons only form? And what does it allow?

Answer 16

1. Matrixs

2. Allows amplification within the cell only

Question 17

What can RNA H do?

Answer 17

It can degrade RNA only if it is in a DNA/RNA complex

Question 18

What does the envelope do?

Answer 18

Protects the capsid while they are moving from cell to cell

Question 19

What is RT?

Answer 19

DNA polymerase that can use RNA or DNA as a template

Question 20

What does integrase act similar to?

Answer 20

Transposase of DNA transposons

Question 21

What does the promoter TATA box do?

Answer 21

Provides binding sites for transcription

Question 22

What does LTR function as?

Answer 22

As a promoter that directs host cell RNA polymerase to initiate transcription at the 5’ nucleotide of the R sequence

Question 23

What does RNA intermediate lack? (2)

Answer 23

1. A promoter at the 5’ end

2. U5 part at the 3’ end

Question 24

What happens if the poly A signal is lost? (2)

Answer 24

1. It will be non-autonomous

2. Wont be able to move from cell to cell

Question 25

What is the LTR solution? (7)

Answer 25

1. A tRNA binds 3' of the U5 2. RT extends to 5' end of RNA 3. RH degrades RNA in RNA/DNA duplex 4. R region of cDNA binds to complementary R region at 3' end of RNA 5. RT extends to the new 5' end 6. RH degrades most of the hybrid RNA 7. PBS region of the 2nd strand cDNA binds to the other PBS region on the 1st strand - RT extends to form a complete dsDNA of the retrotransposons

Question 26

Why should you always use a tRNA compared to other RNAs? (2)

Answer 26

1. Because it is present in all cells 2. Because it is always present - but can use other RNAs

Question 27

What is the most abundant type of transposon in mammals?

Answer 27

Non-LTR transposons | - LINE

Question 28

LINE

Answer 28

Long interspersed elements | - ~6kb

Question 29

SINE

Answer 29

Short interspersed elements | - ~0.3kb

Question 30

What do SINE not contain?

Answer 30

Protein coding regions

Question 31

What do SINE only contain?

Answer 31

Flanking regions

Question 32

What do SINEs use to facilitate their movement?

Answer 32

Proteins

Question 33

What are all SINEs?

Answer 33

Non-autonomous

Question 34

What do SINEs use to amplify?

Answer 34

LINEs encoded machinery

Question 35

Where is the promoter for SINE located?

Answer 35

Downstream but it affects the upstream | - it is part of the transcript

Question 36

What do autonomous transposons only encode? (2)

Answer 36

1. RT 2. Endonuclease - absolutely need this

Question 37

What can the enzymes RT and endonuclease act on? (2)

Answer 37

1. Itself | 2. Other transposons of the same class

Question 38

How do SINES get amplified?

Answer 38

By having RT and endonuclease act on it

Question 39

What 2 thing are coupled in non-LTR transposons movement and amplification?

Answer 39

1. RT | 2. Integration

Question 40

What is not needed in non-LTR transposons movement and amplification?

Answer 40

Integrase enzyme | - integration is done by RT

Question 41

What does movement lead to in non-LRT transposons?

Answer 41

Increase in transposon copy numbers | - because the original copy stays were it is and gets duplicated

Question 42

What are the 11 multistep pathway during non-LTR transposon movement?

Answer 42

1. Binds to any part of the genome where there are some present in the genome 2. Add leaking enzyme 3. Cut the dsDNA in a nik fashion 4. Then allows genomic DNA to separate 5. Base pairing create pairing sites for RT - its job is to create DNA copy for the template 6. At the same time RT stays bound to the other end of the DNA 7. The strand gets flipped around and forms a newly formed DNA strand 8. Switches from RNA template to ssDNA 9. RT switches over and uses DNA strand as a template and moves along 10. All of this is needed because the cellular repair mechanism recognize the breaks and also there is a RNA/DNA hybrids 11. The DNA polymerase comes in a repairs the damage