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Molecular Biology - 3550 > chapter 14: site specific recombination-- exam 2 > Flashcards

chapter 14: site specific recombination-- exam 2 Flashcards

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1
Q

what is site specific recombination?

A

rearrangement between 2 specific DNA sequences

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2
Q

What does site specific combination result in?

A
  • insertion
  • deletion
  • inversion
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3
Q

Site specific recombination requires ______ and ______

A
  • restriction endonucleases
    and
  • ligases
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4
Q

T/f Site specific recombination is isoenergenic and doesn’t require extensive homology

A

true

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5
Q

What is the earliest form of parasitism?

A

Transposition

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6
Q

What is transposition?

A

When transposons move freely between different chromosomes

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7
Q

Where are recombination sites located?

A

at inverted repeats with a non palindromic core

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8
Q

Does the non palindromic core have direction?

A

yes

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9
Q

Describe the direction of the non palindromic core

A
  • recombination with cores in opposite directions lead to inversions
  • recombination with cores in the same directions lead to deletions
  • between 2 separate chromosomes, same direction cores lead to insertions
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10
Q

recombination with cores in opposite directions lead to ______

A

inversions

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11
Q

recombination with cores in the same directions lead to _______

A

deletions

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12
Q

between __________, same direction cores lead to ______

A

2 separate chromosomes ; insertions

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13
Q

Active sites are typically ___ or ___ residues as nucleophile

A

Ser ; Tyr

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14
Q

_ light gray recombinases are active at a time

A

2

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15
Q

site specific reaction is very similar to the process of _____

A

topoisomerases

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16
Q

What are some examples of site-specific recombination?

A
  • plasmid replication
  • viral DNA circularization
  • biotech
  • phase variation
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17
Q

What are bacteriophages?

A

viruses that infect bacteria

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18
Q

What are the 2 pathways of viral infections?

A
  1. lysogenic pathway

2. lytic pathway

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19
Q

LoxP is…

A

site specific recombination loci

- allows for circulation of bacteriophage DNA

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20
Q

What is Salmonella typhimurium?

A

Regulates gene expression via site-specific recombination
•Flagella is a prominent target of mammalian immune systems
•Can change protein types of flagella to avoid host immunity!
•FljB  FliC

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21
Q

Pieces of DNA that move from one part of the genome to the other (donor –> target site)
- can be random or specific

A

Transposons

22
Q

What are the 3 types of transposons?

A
  1. cut and paste
  2. replicative
  3. RNA intermediate (retrotransposon)
23
Q

________ is coded for within the transposable element transposon

A

transposase

24
Q

What 2 things does transposes catalyze?

A
  1. hydrolytic cleavage

2. Transesterification

25
Q

What is a cut and paste transposition?

A

•Double-stranded cuts in donor DNA—must be repaired*
•Liberated DNA attacks target DNA via 3’ –OH groups to form new phosphodiester bonds
•Single-stranded gaps filled in with repetitive DNA
*Donor DNA can be repaired through ligation or recombination repair

26
Q

What are the 2 types of retrotransposons?

A
  1. Long-terminal repeat with extrachromosomal primed retrotransposition
    (LTR (EP))
  2. Non-long-terminal repeat with target-primed retrotransposition
    (Non LTR (TP))
27
Q

LTR (EP) Retrotransposons:

A
  • Transposon with a long-terminal repeat and extrachromosomally primed retrotransposition
  • Long-terminal repeat = repetitive DNA at the termini of transposon between 100 – 5000 bp
  • Extrachromsomally primed = DNA primers come from tRNA (not part of the chromosome)
28
Q

Mechanism of LTR (EP) Retrotransposons:

A
  1. Transposon is transcribed by RNA polymerase  ssRNA transcript
  2. Reverse transcriptase  ds-cDNA
    * •Remember, DNA always requires a primer! In this case . . . tRNA . . . wild!
  3. Circularized by integrase (related to transposase)
  4. Invasion of target DNA
  5. Donor and target both have copy of transposon
    * Reverse transcriptase can make dsDNA out of ssRNA. That is, it can use DNA and RNA as a template.
29
Q

Non-LTR (TP) Retrotransposons

A
  • Transposon without long-terminal repeat, with target-primed retrotransposition
  • Uses part of the ssRNA intermediate as a primer for DNA
30
Q

Bacteria have 3 common classes of transposons, what are they?

A
  1. Insertion sequences
  2. Composite transposons
  3. Complex transposons
31
Q

Generally, do bacterial transposons have RNA intermediates?

A

NO

32
Q

What do Insertion sequences contain?

A

Only DNA sequences necessary for transposition

33
Q

What do composite transposons contain?

A

DNA sequences necessary for transposition and other genes

34
Q

Complex transposons have:

A
  • large genome
  • genes for other processes than transposition
  • act as transposon or bacteriophage DNA
    (lytic and lysogenic pathway_
35
Q

What percent of human DNA in each cell consists of transposons?

A

46%

36
Q

What percent of transposons in human DNA come from retrotransposons?

A

90%

37
Q

What percent of humans retrotransposons in their DNA are LTR vs Non-LTR?

A

LTR: 20%

Non- LTR: 80%

38
Q

Describe LTR retrotransposons:

A
  • Similar to viruses
  • Transcribed with a poly-A tail•Transported to cytoplasm
  • Translated to
  • Gag = structural; creation of VLP
  • Pol = reverse transcriptase
  • Int = integrase
  • Reverse transcribed and brought into the nucleus via VLP
  • dsDNA integrates in new location
39
Q

What are the 2 types of Non-LTR transposons?

A

LINEs and SINEs

40
Q

What does LINEs stand for?

A

Long interspersed nuclear elements

41
Q

What does SINEs stand for?

A

Short interspersed nuclear elements

42
Q

Are LINEs autonomous?

A

Yes

43
Q

Are SINEs autonomous?

A

No

44
Q

Describe LINEs:

A
  • Transcribed to RNA in nucleus
  • RNA translated into cytoplasm
  • Reintegrates DNA into the nucleus
  • Autonomous
45
Q

Describe SINEs:

A

•Transcribed to RNA in nucleus
•RNA translated into cytoplasm
•Reintegrates DNA into the nucleus
- Non-autonomous

46
Q

What is the difference between SINEs and LINEs?

A

SINEs are non-autonomous

47
Q

What are retroviruses?

A

Viruses that contain reverse transcriptase

48
Q

What are the typical genes of retroviruses?

A 
Gag = structural
Pol = reverse transcriptase, integrase, proteases
Env= structural ; allows element to transfer from cell to cell
49
Q

What does viral reverse transcriptase lack?

A

3’ –> 5’ exonuclease activity

50
Q

HIV is a retrovirus that infects ____ cells

A

T

51
Q

What are the drug targets for HIV

A
  • reverse transcriptase

- HIV proteases

52
Q

Why is combination effective in fighting HIV?

A

because there is a very high mutation rate

Molecular Biology - 3550 (8 decks)

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