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Pharmacology 200 > 3 - epigenetic drugs > Flashcards

3 - epigenetic drugs Flashcards

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1
Q

what is epigenetics

A

modification of gene expression rather than the DNA code itself

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2
Q

what are 2 criteria for something to be epigenetic

A

1-change in gene function without mutation

2-heritable

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3
Q

what happens when you change chromatin structure

A

it alters accessibility to transcription factors

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4
Q

what is euchromatin

A

open, accessible, genes on, acetylated histone

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5
Q

what is heterochromatin

A

close, inaccessible, genes off, deacetylated histone

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6
Q

is euchromatin or heterochromatin acetylated

A

euchromatin

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7
Q

is euchromatin or heterochromatin deacetylated

A

heterochromatin

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8
Q

what are two types of histone modification

A

methylation and acetylation

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9
Q

where does methylation and acetylation occur and why

A

on positive residue (lysine, arginine) to neutralize negative charge of DNA

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10
Q

what is changed when there is epigenetic modifications

A

structure of chromatin and its accessibility is changed

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11
Q

where are 2 places that there can be epigenetic modifications

A

DNA or histones

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12
Q

what gets methylated in DNA methylation

A

cytosine

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13
Q

what happens in DNA methylation

A

Methylation of cytosine bases is associated with

transcriptionally inactive DNA, usually recruits histone modifications.

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14
Q

why is epigenetics important (3)

A

because it can turn genes on and off (things like growth, specialized cell types and X-chromosomal inactivation)

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15
Q

what causes skin cells to be so different than hair and brain cells

A

epigenetics!

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16
Q

what type of epigenetic alterations are often found with cancer genes

A

turned off tumor supressor gene or turned on oncogene

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17
Q

how does cancer spread if epigenetic changes arent hertiable

A

no, they are heritable

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18
Q

what often happens to promotors in aging

what does this mean

A

they undergo DNA hypermethylation

-less promotor activity

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19
Q

what often happens to intragenic regions in aging

what does this mean

A

they become hypomethylated

-more intragenic region activity (?)

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20
Q

what two things cause histone methylation and acetylation to change

A

age and environment

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21
Q

what is histone methylation

A

post translational modification where a methyl group is transferred to a histone protein

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22
Q

which part of the histone is methylate

A

the positive residues (lysine arginine) to neutralize charge

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23
Q

what does histone methylation do to the interactions between histones and DNA

A

weakens interactions (neutralized the positive charge)

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24
Q

which amino acid does histone methylated happen to more often

A

lysine more so than arginine

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25
can histone methylation occur on all 4 histones
yes
26
what are the two primary methyltransferase enzyme families
SET1 and SUV family
27
how do histone methyltransferases work
they comsume S-adenosyl methionine (SAM) cofactor to move methyl groups
28
what are two main classes of histone demethylases
LSD type and JHD1 type
29
how do you classify LSD-type vs JHD1-type histone demethylases
based on the cofactor they use
30
which cofactor for LSD-type use
(FAD)-dependent amine oxidase
31
which cofactor for JHD1-type use
Fe(II) and alpha-KG-dependent hydroxylase
32
which histone methylation drug is being tested in cancer
LSD1 inhibitors
33
why are many histone demethylation drugs not used clinically
because they are often non-specific
34
what is tazemetostat
an inhibitor of EZH2 histone methyltranferases
35
what can tazemetostat be used for
hematopoetic malignancies
36
what does tazemetostat do to methylation and chromatin
inhibits histone methylation(methyltransferases), tighter DNA and histone interactions, heterochromatin, turn genes off
37
what do LSD1 inhibitors do to methylation
they inhibit histone demethylation, meaning that there will be more methylation
38
what is histone acetylation
PTM modification that adds acetyl group onto lysine residue of histone proteins
39
where does hsitone acetylation occur
onto lysine
40
what does histone acetylation do to chromatin and why
often activates because it neutralizes the charge so it makes euchromatin
41
does histone acetylation or methylation weaken the histone-DNA attraction
both! (but histone acetylation does most of the time not always)
42
how do histone acetyltransferases work
they transfer acetyl-CoA's (Cofactor) acetyl to lysine on histone
43
which cofactor do histone acetyltransferases use
acetyl-CoA
44
what are the 2 major histone acetyltransferases enzymes
PCAF and P300
45
what do histone deacetylases produce
deacetylated histones and acetate
46
what are the 3 major classes of histone deacetylases
Class 1, 2, 3
47
what do class 1 and 2 histone deacetylases do
use Zn2+ as a cofactor to make a deacetylated histone and acetate
48
what do class 3 histone deacetylases do
sirtuins!! they use NAD+ as their cofactor
49
whata is another name for class 3 histone deacetylases
sirtuins
50
do histone deacetylases make euchromatin or heterochromatin
heterochromatin (remove acetyl, tight, inaccessible)
51
what are the histone acetylation drugs designed to do
inhibit HDAC enzymes
52
how can histone acetylation drugs be used/good for cancer
to reactivate silenced tumor suppressor genes
53
what makes sirtuins different than class 1 and 2
they deacetylate histones and other proteins too
54
what is vorinostat
an inhibitor of Class 1 and 2 histone acetylases
55
what can vorinostat be used for
T cell lymphoma
56
what is DNA methylation
addition of methyl at the 5' position of a cytosine
57
where does most DNA methylation occur
in CGCGCGCGCG regions of DNA
58
what does DNA methylation do to genes
often suppressive by blocking the promotor recognition of a TF BUT it can also activate
59
how does DNA methylation change during DNA replication
enzymes can move and copy methylation but sometimes it doesnt happen
60
does DNA methylation interfere with base pairing
no
61
how do DNA methyltransferases work
by using SAM as a cofactor
62
in general, what does SAM cofactor move
methyl groups
63
what are 3 types of DNA methyltransferases
Dnmt1, Dnmt3a and Dnmt3b
64
what does Dnmt1 do
copies methylation to second DNA strand if the first one has it
65
what does Dnmt3a and Dnmtb do
can methylate wherever they want
66
which Dnmt acts as maintenance (making sure methylation is preserved during replication)
Dnmt1
67
what are 2 ways that demethylation occurs
dilution in DNA replication or actively from enzymes
68
what are 2 enzymes that do DNA demethylation
activation induced cytidine deaminase enzyme (AID) and Ten Eleven Translocation enzymes (TET)
69
how do most DNA methylation drugs work
inhibit Dnmt enzymes
70
how are DNA methylation drugs good for cancer/effective
reactivate silenced transcription factors
71
what is decitabine
inhibitor of Dnmts
72
what does Vitamin C do
activate the TET DNA demethylase enzymes
73
how do histone and DNA modifications work together
they help direct open vs closed chromatin
74
which enzyme acts as a histone methyltransferase
SET1 and SUV1
75
which enzyme required FAD as a cofactor
LSD1
76
which enzyme required Fe(II) and alpha-JG-dependent hydroxylase as a cofactor
JHD1-type histone demethylases
77
which enzyme required acetyl-CoA as a cofactor
CAF and P300 which are histone acetyltransferases
78
which enzyme required Zn2+ as a cofactor
Class 1 and 2 histone deacetylases
79
which enzyme required NAD+ as a cofactor
class 3 histone deacetylases - sirtuins
80
what is LSD use as cofactor
FAD
81
what is LSD-type do
histone demethylase
82
what is JHD1 type cofactor
Fe and KG hydroxylase
83
what does JHD1 do
histone demethylase
84
what cofactr do SUV and SET1 need
SAM
85
what do SUV abd SET1 do
histone methyltransferase
86
what do PCAF and P300 use as cofactor
acetyl coa
87
what do PCAF and P300 do
histone acetyltransferase
88
what cofactor do class 1 and 2 use
zinc
89
what do class 1 2 3 (sirt) do
histone deacetylase
90
what co factor do sitruins class 3 use
NAD
91
what does vorinostat do
inhibit class 1 2 deacetylases
92
what does dnmt family do
DNA methyltransferases
93
what ofactor do dnmt fammy use
SAM
94
what does AID and TET do
DNA demetyhlase
95
what does Vit C do
activates TET demthylase
96
what does decitabine do
inhibits dnmts
97
what is the goal of decitabine
reactive silenced tumor suppressor genes

Pharmacology 200 (29 decks)

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