GAG WK2 Flashcards
(80 cards)
1
Q
What is epigenetics?
A
- changes in gene expression w/o altering the DNA sequence
2
Q
What is epigenetics influenced by
A
lifestyle and environment
3
Q
What is the role of histone modifications in gene expression?
A
- they regulate how tightly or loosely DNA is wrapped around histones
- affect gene expression availability
4
Q
What part of the histone is modified in epigenetic regulation?
A
- the exposed tails
- the N-terminals
5
Q
How do histone tails interact with DNA?
A
positively charged N-terminals attract negatively charged DNA
6
Q
What is histone acetylation?
A
- addition of an acetyl group to histones
7
Q
What is the effect of histone acetylation
A
- promotes gene expression by making DNA more accessible
8
Q
What enzyme is responsible for histone acetylation?
A
- HAT enzyme (Histone Acetyltransferase)
9
Q
How does histone acetylation happen/work
A
- Acetylation reduces the positive charge of histones
- decreasing interaction w/ negatively charged DNA
- less condensed –> DNA more accessible
10
Q
What is the result of histone acetylation?
A
a relaxed chromatin structure, allowing active gene transcription
11
Q
What enzyme removes acetyl groups from histones?
A
- HDAC (Histone Deacetylase)
12
Q
What is histone deacetylation
A
the removal of an acetyl group from histone
13
Q
What happens during histone deacetylation?
A
- HDAC removes acetyl groups
- histones tails become more positive
- DNA is pulled towards histone (higher affinity)
- more chromatin condensation –> DNA is less accessible
14
Q
What is histone methylation?
A
addition of 1 or more methyl groups to histones
15
Q
What enzyme adds methyl groups to histones?
A
KMT (Methyltransferase)
16
Q
What enzyme removes methyl groups from histones?
A
KMD (Demethylase)
17
Q
What effect does methylation of histone H3 at lysine 4 (H3K4me3) have on gene expression?
A
gene activation
18
Q
What effect does methylation of histone H3 at lysine 9 (H3K9me3) or lysine 27 (H3K27me3) have on gene expression?
A
gene silencing
19
Q
What is the result of histone methylation
A
it can either silence or enhance gene expression
20
Q
How do histone modifications affect cancer?
A
Mutations in enzymes that modify histones can change chromatin structure
21
Q
What happens to tumor-suppressing genes in cancer due to abnormal histone modifications?
A
- can be silenced
- inhibits control of cell growth
- resulting in tumour development
22
Q
What role do oncogenes play in cancer related to histone modifications?
A
- become over-expressed
- leading to increased cell division
23
Q
What is DNA methylation
A
methyl group os added to cytosine bases at CpG sites
24
Q
What are CpG methylation islands?
A
regions of DNA with a high frequency of CpG sites
25
Where are most CpG sites/islands found
- near promoter region
26
Why are most CpG sites found near promoter region
because it is where genes that are always active
27
What is the normal state of CpG islands in healthy cells?
- unmethylated
- to promote gene expression
28
What happens when CpG islands are abnormally methylated?
- genes are silenced
- linked to cancer
29
How does DNA methylation cause gene silencing?
1. methyl groups change DNA structure
2. transcription factors can't bind/recognise DNA
3. methyl-CpG-binding proteins cause chromatin condensation --> gene silencing
30
How is DNA methylation maintained during replication?
- DNMT1 copies methylation pattern to new DNA during replication
- it is passed to daughter cells
31
Why is the maintenance of DNA methylation important?
ensures the correct genes are expressed in the right tissue
32
What is de novo methylation?
- the addition of new methylation patterns
- new gene expression
33
What enzyme is responsible for de novo methylation?
DNMT3A and DNMT3B
34
What are the 2 cycles of demethylation and methylation for gene expression regulation?
- clearing paternal marks
- re-establishing new patterns
35
Explain what is meant by "clearing paternal marks" in DNA methylation
- methylation from parent is remove to reset embryo's gene expression
36
Explain what is meant by "re-establishing new patterns" in DNA methylation
- new methylation patterns are set to control which genes are active in which type of cells
37
What is genomic imprinting
when only one allele is active from either mom or dad, whilst the other is silenced
38
Why does genomic imprinting happen
- some genes need to come from only 1 parent to work
- if both alleles are active --> problems
39
What is an example of genomic imprinting
X-inactivation
40
Explain what X-inactivation is
- only in females
- each cell randomly inactivates an X chromosome
41
How does X-inactivation work
- each cell inactives an X chromosome
- the inactivated X chromosome by DNA methylation condenses into Barr body
42
What is the function of X-inactivation
- prevent there being too many X linked proteins
43
What is demethylation and its role in gene transcription?
- removes methyl groups from DNA
- allows for the resumption of transcription (restart)
- promotes gene expression
44
What is EWAS and its purpose in ALS research?
finds epigenetic markers (esp. DNA methylation)
45
What are the 2 main methods used to for EWAS
- nanopore sequencing
- base-swapping
46
Explain how nanopore sequencing helps identify epigenetic markers
detects methylation by reading DNA w/o modifications
47
Explain how base-swapping helps identify epigenetic markers
- compares treated DNA w/ original DNA
- If C turns to T = cyctosine is unmethylated
- If C stays the same = cytosine is methylated
48
What is RNA splicing?
the removal of introns in gene
49
Why must introns be removed?
Introns don't code for proteins
50
What happens if introns are not removed
- cause premature stop codons
- produce mutated polypeptide
51
Where does an intron start?
at the donor site/5’ end with a GU sequence
52
Where does an intron end
ends at the acceptor site/3’ end with an AG sequence
53
Where is the branch site ?
- within intron
- has an adenine
54
What role do snRNAs play in RNA splicing?
mediate the joining of exons
55
What is the function of snRNP
facilitates RNA cutting and exon joining
56
What happens first in RNA splicing?
U1-snRNP binds to the 5’ donor site
57
What happens second in RNA splicing?
U2-snRNP binds to the branch site (Adenine)
58
What is the nucleophilic attack during splicing?
- The -OH group at the branch site
performs a nucleophilic attack on the 5’ donor site
- forming a lariat intermediate
59
How do exons join together?
The 5’ exon attacks the 3’ acceptor site, joining the exons together.
60
What happens to the lariat after splicing?
- The lariat stays bound to tri-snRNP
- then released and degraded
- snRNPs are recycled
61
What is the function of U1-snRNP
binds to 5' donor site
62
What is the function of U2-snRNP
binds to branch site
63
What is the function of U2-snRNP & U6-snRNP complex
bring together exons
64
What happens after U2-snRNP binds to branch site
- U2-snRNP & U6-snRNP come together
- U6-snRNP replaces U1-snRNP at 5'
- U2-snRNP & U6-snRNP form catalytic core of spliceosome
- catalyse the nucleophilic attack to form a lariat
65
What is the function of SR proteins
- recognise splicing enhancers on mRNA
- acts as anchor for spliceosome
66
How does splicing add diversity
- allows different versions of mRNA transcripts and proteins to be produced from the same gene
67
Provide an example of RNA editing.
In the ApoB gene, RNA editing introduces a stop codon that alters protein structure
68
What initiates RNA degradation?
RNA degradation begins with the gradual shortening of the poly-A tail by an exonuclease
69
What happens to the 5' cap during RNA degradation?
- 5' cap is removed
- exposing both ends of mRNA
- exonuclease can work on both ends
70
What are P-bodies?
- compartments rich in exonucleases that degrade mRNA
71
What is the function of P-bodies in relation to mRNA?
- P-bodies can store mRNA protected by proteins for later use or degrade it if not used
72
Why are P-bodies critical in neurons?
- important in local protein synthesis
- essential for maintaining plasticity in neuronal processes
73
What are stress granules?
store mRNA when cells are stressed and unable to produce new proteins
74
What happens to mRNA in stress granules when stress subsides?
stored mRNA is released back into the cytoplasm for translation
75
How are stress granules related to neuronal diseases?
can lead to protein and RNA aggregation in neurons
76
What are exosomes?
structures made up of proteins that degrade RNA
77
How does RNA degradation occur in exosomes?
1. RNA is captured by RNA-binding proteins at the top of the exosome
2. fed to ribonucleases that degrade it.
78
What are the types of exosomes?
- nuclear exosomes
- cytosolic exosomes
79
What is the function of nuclear exosomes?
degrade improperly modified RNA in the nucleus
80
What is the function of cytosolic exosomes
target defective mRNA in the cytoplasm for degradation
