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Pharmacology 200 > 3 - gene editing drugs > Flashcards

3 - gene editing drugs Flashcards

1
Q

what is genomics

A

the branch of biology dealing with aspects of the genome (all genetic info in an organism)

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2
Q

is genomics descriptive

A

yes

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3
Q

what is predictive modelling

A

predicting things like pharmacogenetics and susceptibility to disease

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4
Q

how do you do gene sequencing (2)

A

genome wide association studies and classification of organisms

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5
Q

what is pharmacogenetics

A

use genes to see how you will be affected by drugs

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6
Q

what is genome wide association study

A

compare two big populations, one with gene and one without

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7
Q

what are monogenic diseases

A

diseases caused by a mutation in a single gene

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8
Q

what are more monogenenic diseases (gain vs loss of function)

A

loss of function

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9
Q

is it easier to find small molecule activators in inhibitors

A

hard to find hinhibitors, harder to find activators

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10
Q

what are 3 drawbacks to gene editing

A

off-target effects, mutations, irreversibility

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11
Q

what do Zinc fingers bind to

A

specific DNA triplet sequences

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12
Q

what are most zinc fingers part of

A

transcription factors

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13
Q

can all triplets be recognized by natural zinc fingers?

A

no (so we engineered new ones)

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14
Q

how many zinc fingers would be used to target a 9 bp sequence

A

3

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15
Q

what is a zinc finger nuclease

A

two zinc finger arrays linked to subunits of the heterodimeric Fok1 endonuclease

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16
Q

what must the heterodimeric Fok1 endonucleases have to work

A

both of the 2 subunits to come together

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17
Q

what do endonucleases do

A

cut DNA internally

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18
Q

is heterodimeric Fok1 endonucleases specific to where it cuts?

A

no, so you attach them to zinc fingers to guide them

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19
Q

where do the zinc finger nucleases bind

A

to the left and right sequences surrounding the spacer where the cut occurs

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20
Q

where does a TALE domain bind

A

to 1bp of DNA

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21
Q

how do TALEs target long sequences of DNA

A

they can be linked

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22
Q

how is it determined where TALEs bind

A

two amino acids determine which specific base is bound (all the other amino acids are constant, just 2 variants)

23
Q

what is TALEN

A

two tale arrays linked to subunits of the heterodimeric Fok1 endonuclease

24
Q

is protein engineering required for TALENs

A

NOOOO (each base can be targeted by a particular domain)

25
Q

what does non-homologous end joining to do genes

A

insertions or deletions that knockout / inactivation a gene

26
Q

what are 2 DNA repair mechanisms

A

non homologous end joining and homologous recombination

27
Q

what does homologous recombination to do genes

A

knock-in or gene editing by supplying repair DNA

28
Q

how does non homologous end joining often cause a knockout of genes

A

cut makes staggered overhands, they get degraded(remove stuff) then fused together then boom deletion

29
Q

how can homologous recombination be used to make a new gene

A

the DNA is cut then resupplied with new template DNA

30
Q

what is CRISPR in prokaryotes part of

A

their prokaryotic immune system that defends against viruses

31
Q

what are the 4 steps in CRISPR immune stuff in viruses

A

1-invasion
2-adaptation
3-production
4-targeting

32
Q

what happens in invasion of CRISPR

A

the virus gets into the bacterial cell

33
Q

what happens in adaptation stage of CRISPR

A

DNA from bacteriophage is stored into the CRISPR sequence

34
Q

what happens in production stage of CRISPR

A

CRISPR RNA is made from the memory locus that is complementary to the bacteriophage

35
Q

what happens in targeting stage of CRISPR

A

endonuclease Cas9 binds to RNA to find the homologous sequence on the DNA of the bacteriophage then kills it

36
Q

what is the difference with Cas9 and CRISPR

A

they the same

37
Q

what are 3 main components of CASRP Cas9

A

Cas9 endonuclease,

crRNA with 20bp sequence used to target, trans-activating crRNA

38
Q

what is the PAM sequence

A

NGG

Cas9 has a specificity for it

39
Q

what is the first step of CRISPR Cas9 cleavage

A

Cas9 binds to PAM

40
Q

what happens after Cas9 binds to PAM

A

cas9 tries to pair guide RNA with DNA

41
Q

what are the two nuclease domains of cas9

A

RuvC and HNH

42
Q

what happens after cas9 pairs guide RNA with DNA

A

the two nuclease domains (RuvC and HNH) cut the DNA to have a double-stranded break

43
Q

what happens after the RuvC and HNH cut the DNA

A

non homologous end joining or homologous recombination come to fix it

44
Q

what are the 3 important steps in determining the 20-bp sequence to target

A

1-identify PAM (NGG) sequence in DNA you want to target
2-count 20 nucleotides upstream PAM to find 5’ start of sgRNA target sequence
3- determine the actual sgRNA sequence

45
Q

what is sgRNA

A

CRISPR RNA

46
Q

what is PAM sequence

A

NGG

47
Q

why cant cas9 get into cells easily

A

they are large and complex and impermeable to the cell membrane

48
Q

what are 3 ways you can get gene editing tools into cells

A

1-viruses
2-physical disruption of membrane (small needle)
3-chemical coating(attach to nanoparticle to get it through the membrane)

49
Q

what could happen if you cleave DNA

A

induce DNA-damage response in cell, causing cell death

50
Q

what does ex-vivo mean

A

therapy is performed outside the body

51
Q

what is in vivo

A

when therapy is treated directly in the body

52
Q

what is somatic cell

A

cell that is not reproductive and not passed on

53
Q

what is germ-line cell

A

cell that is reproductive and passed on

54
Q

what is the sequence of events in Cas9 DNA cleavage reaction *3)

A

PAM binding
crDNA hybridization
activation of nucleases

Pharmacology 200 (29 decks)

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