Midterm 2 - Notes 1 (Part 2) Flashcards
What did the predecessor acquire? (2)
- Reverse transcriptase
2. RnaseH
RT
Reverse transcriptase
RH
RnaseH
What are RT and RH?
They are types of enzymes
What do LTR retrotransposons acquire? (2)
- LTRs
- A protease
- processes primary protein to RT and RH
What do retroviruses acquire?
Envelope proteins
- allowing them to leave the cell
What do non-LTR retrotransposons gain and allow?
Envelope proteins that allow to encapsulate the complex with the proteins and RNAs
What are LINEs?
Non-LTR retrotransposons
What can non-LTR retrotransposons do?
They can leave the cell and form viral particles
How do retroviruses move?
They move from cell to cell
How do retro-transposons move?
Within the cell
What do LTR-transposon and retroviruses share?
Mechanism of movement and amplification
What are RNA and proteins made by in the lifecycle of retroviruses and LTR transposons?
Regular cellular transcription/translation machinery
- RNA transferase
- can use DNA as a template
What kind of proteins do viruses only have?
Enveloped proteins
What do enveloped proteins allow?
Movement from cell to cell
What do retrotransposons only form? And what does it allow?
- Matrixs
2. Allows amplification within the cell only
What can RNA H do?
It can degrade RNA only if it is in a DNA/RNA complex
What does the envelope do?
Protects the capsid while they are moving from cell to cell
What is RT?
DNA polymerase that can use RNA or DNA as a template
What does integrase act similar to?
Transposase of DNA transposons
What does the promoter TATA box do?
Provides binding sites for transcription
What does LTR function as?
As a promoter that directs host cell RNA polymerase to initiate transcription at the 5’ nucleotide of the R sequence
What does RNA intermediate lack? (2)
- A promoter at the 5’ end
2. U5 part at the 3’ end
What happens if the poly A signal is lost? (2)
- It will be non-autonomous
2. Wont be able to move from cell to cell
What is the LTR solution? (7)
- A tRNA binds 3’ of the U5
- RT extends to 5’ end of RNA
- RH degrades RNA in RNA/DNA duplex
- R region of cDNA binds to complementary R region at 3’ end of RNA
- RT extends to the new 5’ end
- RH degrades most of the hybrid RNA
- 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
Why should you always use a tRNA compared to other RNAs? (2)
- Because it is present in all cells
- Because it is always present
- but can use other RNAs
What is the most abundant type of transposon in mammals?
Non-LTR transposons
- LINE
LINE
Long interspersed elements
- ~6kb
SINE
Short interspersed elements
- ~0.3kb
What do SINE not contain?
Protein coding regions
What do SINE only contain?
Flanking regions
What do SINEs use to facilitate their movement?
Proteins
What are all SINEs?
Non-autonomous
What do SINEs use to amplify?
LINEs encoded machinery
Where is the promoter for SINE located?
Downstream but it affects the upstream
- it is part of the transcript
What do autonomous transposons only encode? (2)
- RT
- Endonuclease
- absolutely need this
What can the enzymes RT and endonuclease act on? (2)
- Itself
2. Other transposons of the same class
How do SINES get amplified?
By having RT and endonuclease act on it
What 2 thing are coupled in non-LTR transposons movement and amplification?
- RT
2. Integration
What is not needed in non-LTR transposons movement and amplification?
Integrase enzyme
- integration is done by RT
What does movement lead to in non-LRT transposons?
Increase in transposon copy numbers
- because the original copy stays were it is and gets duplicated
What are the 11 multistep pathway during non-LTR transposon movement?
- Binds to any part of the genome where there are some present in the genome
- Add leaking enzyme
- Cut the dsDNA in a nik fashion
- Then allows genomic DNA to separate
- Base pairing create pairing sites for RT
- its job is to create DNA copy for the template - At the same time RT stays bound to the other end of the DNA
- The strand gets flipped around and forms a newly formed DNA strand
- Switches from RNA template to ssDNA
- RT switches over and uses DNA strand as a template and moves along
- All of this is needed because the cellular repair mechanism recognize the breaks and also there is a RNA/DNA hybrids
- The DNA polymerase comes in a repairs the damage
