Chapter 19 - Unit 4 Flashcards
(64 cards)
1
Q
define epigenetic
A
when changes in gene expression are independent than the changes in DNA sequence
2
Q
what are the three major epigenetic mechanisms
A
- chromatin remodeling
- DNA methylation
- regulation by noncoding RNA
3
Q
how can chemical modifications be inherited in an epigenetic manor
A
- histone modifications ans DNA methylation
2. random distributions of old and new histones during DNA replication
4
Q
how do you get cytosine replication on both strands to occur
A
- have both strands of DNA have cytosine methylated
- DNA replication occurs
- no have two dsDNA strands but now only one side of each has cytosine methylated
- DNA methyltransferase occurs
- a methyl group was added to both dsStrands of DNA to the side that was missing it (once completely methylated, replication takes place)
- repeat
5
Q
what is chromatin
A
he way the EUK DNA is packaged, contain chromosomes that are mad eup of DNA and chromosomal proteins
6
Q
what are the two types of chromatins
A
- euchromatin
2. heterochromatin
7
Q
euchromatin characteristics
A
- less compacted (loose)
- transcriptionally active
8
Q
heterochromatin characteristics
A
- more compacted
- transcriptionally off
- two types (constitutive and facultative)
9
Q
constitutive heterochromatin charactertistics
A
- always compact
- transcriptionally off
EX: centromere, telomeres
10
Q
facultative heterochromatin characteristics
A
- can switch between being a euchromatin state or a heterochromatin state
EX: X-inactivation
11
Q
what are histones
A
small, basic positive proteins
12
Q
what makes up 20-30% of histones and where do they bind
A
lysine and arginine that bind to DNAs minor groove
13
Q
what is a nucleosome composed of
A
composed of DNA wrapped around a histone core
14
Q
what are open promoters associated with
A
- constitutive genes (genes that are always being expressed)
- NDRs (nucleosome depleted regions; no nucleosomes present)
- enhancer sequences
- activator proteins
- histone variants (H2AZ: that are readily removed before transcription)
15
Q
what are covered promoters associated with
A
regulated genes
16
Q
what allows for genes to be transcribed through a covered promoter
A
- chromatin remodeling complexes modify nucleosomes to go from a closed chromatin state to an open chromatin state
17
Q
what does it mean when a nucleosome is in a closed chromatin state
A
- DNase I is insensitive
- not a lot of exposed DNA, so not a lot of pieces are made
18
Q
what does it mean when a nucleosome is in a open chromatin state
A
- DNase is sensitive
- there is more exposed DNA which means that more pieces will be made
19
Q
when EUK DNA is packed into chromatin how does that affect other aspects
A
DNA is not readily accessibly to RTFs and the transcriptional machinery
20
Q
what are the different types of chromatin remodeling
A
- nucleosome modification
2. histone modification
21
Q
what is nucleosome modification and what is carried out by
A
when the nucleosome is modified and it is carried out by ATP-dependent chromatin remodeling complexes
22
Q
what are the three ways that nucleosomes can be modified and how do they modify them
A
- change in nucleosome position= can change relative positions of them or can change in the spacing between them
- evict histones= histone octamers are removed
- add histone variants= replaces histones with ones that are more ready
23
Q
where do histone modifications take place
A
on histone tails
24
Q
what are the types of histone modifications
A
all are post-transcriptional
- acetylation
- methylation
- phosphorylation
25
what is the pattern of histone modification know as
histone code
26
what do the different patterns of histone modification result in
they result in different levels of chromatin compaction to hide or expose genes for expression
27
what do histone acetyltransferases (HATs) do
They transfer acetyl groups onto histones more specifically onto the lysine group
- when its lysine is neutral between the histone and DNA, DNA loosens up and allows for transcription to occur
28
what do histone deacetylases (HDACs) do
They remove acetyl groups from the lysine groups
- when a gene is being transcribe and is done, HDACs come in and remove the acetyl group allow for DNA to become compacted again, transcription stops
29
what does histone methylation do
depending on the number of methyl groups added to lysine and arginine, it creates binding sites for other proteins to activate or repress gene expression
it doesn't change the charge
30
what do histone methyltransferases (HMTs) do
they add methyl groups to LYS and ARG
31
what do histone demethylases (HDMs) do
they remove methyl groups from LYS and ARG
32
what does phosphorylation of aa do
they add negative charges to various aa, meaning causing repulsion between the histone and DNA because they are both negatively charged; loosening DNA and histone interactions
33
what does the enzyme kinase do
it adds phosphate groups to aa
34
what does the enzyme phosphotase do
they remove phosphate groups from aa
35
what do chromatin readers, writers, and erasers do
they tell the cell whether or not to transcribe a gene
36
what are writers and what do they do
a protein that add chemical groups
EX: histone acetyl transferases, histone methyl transferases, and kinases
37
what are readers and what do they do
they are proteins that determine what the covalent modification pattern means by bonding to the modified histones
38
what are erasers and what do they do
they are proteins that remove chemical groups after a gene has been transcribed
EX: histone deacetylases, histone demethylases, and phosphatases
39
what is DNA mehtylation and where does it occur
when methyl groups are added onto DNA on cytosines from the CpG islands by DNA methyltransferases (DNMTs)
40
where can CpG islands most likely be found and how long are they
near many gene promoters and are about 1,000-2,000 bp in length
41
when the cytosines from the CpG islands are unmethylated how does it affect the gene
the gene is active
42
when the cytosines from the CpG islands are methylated how does it affect the gene
the gene is inactive
43
does DNA methylation typically increase or decrease gene expression
decrease
44
what are the two possible ways that DNA methylation can inhibit transcription
1. add methyl groups, preventing activators from binding to CpG island
2. add methyl groups, methyl-CpG-binding proteins (MECPs) bind to them, recruiting HDACs, which remove acetyl groups from LYS making the DNA compact, which means no transcription
45
what causes rett syndrome
a defect in the methyl-CpG-binding protein-2
46
what is rett syndrome
a neurodevelopmental disorder than includes a deceleration of head growth and small hands, and feet (something about autism spectrum)
fatal in males, so it only occurs in females
47
what does monoallelic expression by imprinting mean
it means that only one of the two alleles of the same gene is expressed and the other is silenced (imprinted) (associated with DNA methylation)
48
what does imprinting entail
essentially a DNA segment is "marked" meaning methyl groups are attached to it, this mark is retained throughout the individuals lifetime ao its silenced
49
what is the role of imprinting control regions
they act as enhancer-blocking insulators when bound by the protein CTC-binding factor (CTCF), and it prevents IGF2 from being transcribed by the maternal copy in normal conditions
50
H19 gene normal imprinting pattern
maternal copy= active due to ICR being unmethylated and preventing IGF2
paternal copy= inactive because the ICRs are methylated
51
IGF-2 gene normal imprinting pattern
maternal copy= inactive
| paternal copy= active
52
h19 and IGF-2 genes in BWS imprinting pattern
H19:
maternal and paternal copy= inactive
IGF-2:
maternal and paternal copy= active
this is because the ICRs are methylated
53
what four conditions are examples of parent-of-origin monoallelic expression by imprinting
1. Beckwith-Wiedemann syndrome (lateralised; overgrowth of tissues) (can be seen in placenta and the fetus)
2. Silver-Russell syndrome (SGA and postnatal growth failure; body asymmetry)(can be seen in placenta and the fetus)
3. Angelman Syndrome
4. Prader-Willi syndrome
54
h19 and IGF-2 genes in SRS imprinting pattern
H19:
maternal and paternal copy= active
IGF-2:
maternal and paternal copy= inactive
this is because the ICRs are unmethylated
55
define epimutations
mutations of the genetic patterns or epigenetic modifications
56
what are two examples of epimutations
1. BWS
2. SRS
* in DNA methylation especially in ICR
57
AS gene normal imprinting pattern
maternal copy= active in brains
| paternal copy= silent
58
PWS gene normal imprinting pattern
maternal copy= silent
| paternal copy= active in brain
59
Stress Induced Behaviors in Rats
| low maternal nurturing outcomes
- decreased serotonin
- decreases histone aceylation
- increases DNA methylation
* stressed pups and end up being the same as their mother
60
Stress Induced Behaviors in Rats
| high maternal nurturing outcomesar
- increases serotonin
- increases histone aceylation
- decreases DNA methylation
* no stressed pups and end up being the same as their mother
61
X-X pairing. counting/choice
| -----------------------> results in........
random x chromosome inactivation
active and inactive or vise versa
62
No X-X pairing. aberrant counting/choice
| -------------------------------------> results in........
chaotic x chromosome inactivation
active and active or active and inactive or inactive and inactive
63
transgene blocks X-X pairing. Failed X counting/choice
| -----------------------------------> results in........
no x chromosome inactivation
64
if you delete the Tsix region on an X chromosome what happens
you wouldn't get any pairings on the X chromosome
