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GAG WK2 Flashcards

1
Q

What is epigenetics?

A
  • changes in gene expression w/o altering the DNA sequence
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2
Q

What is epigenetics influenced by

A

lifestyle and environment

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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
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4
Q

What part of the histone is modified in epigenetic regulation?

A
  • the exposed tails
  • the N-terminals
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5
Q

How do histone tails interact with DNA?

A

positively charged N-terminals attract negatively charged DNA

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6
Q

What is histone acetylation?

A
  • addition of an acetyl group to histones
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7
Q

What is the effect of histone acetylation

A
  • promotes gene expression by making DNA more accessible
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8
Q

What enzyme is responsible for histone acetylation?

A
  • HAT enzyme (Histone Acetyltransferase)
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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
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10
Q

What is the result of histone acetylation?

A

a relaxed chromatin structure, allowing active gene transcription

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11
Q

What enzyme removes acetyl groups from histones?

A
  • HDAC (Histone Deacetylase)
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12
Q

What is histone deacetylation

A

the removal of an acetyl group from histone

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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
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14
Q

What is histone methylation?

A

addition of 1 or more methyl groups to histones

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15
Q

What enzyme adds methyl groups to histones?

A

KMT (Methyltransferase)

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16
Q

What enzyme removes methyl groups from histones?

A

KMD (Demethylase)

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17
Q

What effect does methylation of histone H3 at lysine 4 (H3K4me3) have on gene expression?

A

gene activation

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18
Q

What effect does methylation of histone H3 at lysine 9 (H3K9me3) or lysine 27 (H3K27me3) have on gene expression?

A

gene silencing

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19
Q

What is the result of histone methylation

A

it can either silence or enhance gene expression

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20
Q

How do histone modifications affect cancer?

A

Mutations in enzymes that modify histones can change chromatin structure

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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
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22
Q

What role do oncogenes play in cancer related to histone modifications?

A
  • become over-expressed
  • leading to increased cell division
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23
Q

What is DNA methylation

A

methyl group os added to cytosine bases at CpG sites

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24
Q

What are CpG methylation islands?

A

regions of DNA with a high frequency of CpG sites

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25
Q

Where are most CpG sites/islands found

A
  • near promoter region
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26
Q

Why are most CpG sites found near promoter region

A

because it is where genes that are always active

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27
Q

What is the normal state of CpG islands in healthy cells?

A
  • unmethylated
  • to promote gene expression
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28
Q

What happens when CpG islands are abnormally methylated?

A
  • genes are silenced
  • linked to cancer
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29
Q

How does DNA methylation cause gene silencing?

A
  1. methyl groups change DNA structure
  2. transcription factors can’t bind/recognise DNA
  3. methyl-CpG-binding proteins cause chromatin condensation –> gene silencing
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30
Q

How is DNA methylation maintained during replication?

A
  • DNMT1 copies methylation pattern to new DNA during replication
  • it is passed to daughter cells
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31
Q

Why is the maintenance of DNA methylation important?

A

ensures the correct genes are expressed in the right tissue

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32
Q

What is de novo methylation?

A
  • the addition of new methylation patterns
  • new gene expression
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33
Q

What enzyme is responsible for de novo methylation?

A

DNMT3A and DNMT3B

34
Q

What are the 2 cycles of demethylation and methylation for gene expression regulation?

A
  • clearing paternal marks
  • re-establishing new patterns
35
Q

Explain what is meant by “clearing paternal marks” in DNA methylation

A
  • methylation from parent is remove to reset embryo’s gene expression
36
Q

Explain what is meant by “re-establishing new patterns” in DNA methylation

A
  • new methylation patterns are set to control which genes are active in which type of cells
37
Q

What is genomic imprinting

A

when only one allele is active from either mom or dad, whilst the other is silenced

38
Q

Why does genomic imprinting happen

A
  • some genes need to come from only 1 parent to work
  • if both alleles are active –> problems
39
Q

What is an example of genomic imprinting

A

X-inactivation

40
Q

Explain what X-inactivation is

A
  • only in females
  • each cell randomly inactivates an X chromosome
41
Q

How does X-inactivation work

A
  • each cell inactives an X chromosome
  • the inactivated X chromosome by DNA methylation condenses into Barr body
42
Q

What is the function of X-inactivation

A
  • prevent there being too many X linked proteins
43
Q

What is demethylation and its role in gene transcription?

A
  • removes methyl groups from DNA
  • allows for the resumption of transcription (restart)
  • promotes gene expression
44
Q

What is EWAS and its purpose in ALS research?

A

finds epigenetic markers (esp. DNA methylation)

45
Q

What are the 2 main methods used to for EWAS

A
  • nanopore sequencing
  • base-swapping
46
Q

Explain how nanopore sequencing helps identify epigenetic markers

A

detects methylation by reading DNA w/o modifications

47
Q

Explain how base-swapping helps identify epigenetic markers

A
  • compares treated DNA w/ original DNA
  • If C turns to T = cyctosine is unmethylated
  • If C stays the same = cytosine is methylated
48
Q

What is RNA splicing?

A

the removal of introns in gene

49
Q

Why must introns be removed?

A

Introns don’t code for proteins

50
Q

What happens if introns are not removed

A
  • cause premature stop codons
  • produce mutated polypeptide
51
Q

Where does an intron start?

A

at the donor site/5’ end with a GU sequence

52
Q

Where does an intron end

A

ends at the acceptor site/3’ end with an AG sequence

53
Q

Where is the branch site ?

A
  • within intron
  • has an adenine
54
Q

What role do snRNAs play in RNA splicing?

A

mediate the joining of exons

55
Q

What is the function of snRNP

A

facilitates RNA cutting and exon joining

56
Q

What happens first in RNA splicing?

A

U1-snRNP binds to the 5’ donor site

57
Q

What happens second in RNA splicing?

A

U2-snRNP binds to the branch site (Adenine)

58
Q

What is the nucleophilic attack during splicing?

A
  • The -OH group at the branch site
    performs a nucleophilic attack on the 5’ donor site
  • forming a lariat intermediate
59
Q

How do exons join together?

A

The 5’ exon attacks the 3’ acceptor site, joining the exons together.

60
Q

What happens to the lariat after splicing?

A
  • The lariat stays bound to tri-snRNP
  • then released and degraded
  • snRNPs are recycled
61
Q

What is the function of U1-snRNP

A

binds to 5’ donor site

62
Q

What is the function of U2-snRNP

A

binds to branch site

63
Q

What is the function of U2-snRNP & U6-snRNP complex

A

bring together exons

64
Q

What happens after U2-snRNP binds to branch site

A
  • 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
Q

What is the function of SR proteins

A
  • recognise splicing enhancers on mRNA
  • acts as anchor for spliceosome
66
Q

How does splicing add diversity

A
  • allows different versions of mRNA transcripts and proteins to be produced from the same gene
67
Q

Provide an example of RNA editing.

A

In the ApoB gene, RNA editing introduces a stop codon that alters protein structure

68
Q

What initiates RNA degradation?

A

RNA degradation begins with the gradual shortening of the poly-A tail by an exonuclease

69
Q

What happens to the 5’ cap during RNA degradation?

A
  • 5’ cap is removed
  • exposing both ends of mRNA
  • exonuclease can work on both ends
70
Q

What are P-bodies?

A
  • compartments rich in exonucleases that degrade mRNA
71
Q

What is the function of P-bodies in relation to mRNA?

A
  • P-bodies can store mRNA protected by proteins for later use or degrade it if not used
72
Q

Why are P-bodies critical in neurons?

A
  • important in local protein synthesis
  • essential for maintaining plasticity in neuronal processes
73
Q

What are stress granules?

A

store mRNA when cells are stressed and unable to produce new proteins

74
Q

What happens to mRNA in stress granules when stress subsides?

A

stored mRNA is released back into the cytoplasm for translation

75
Q

How are stress granules related to neuronal diseases?

A

can lead to protein and RNA aggregation in neurons

76
Q

What are exosomes?

A

structures made up of proteins that degrade RNA

77
Q

How does RNA degradation occur in exosomes?

A
  1. RNA is captured by RNA-binding proteins at the top of the exosome
  2. fed to ribonucleases that degrade it.
78
Q

What are the types of exosomes?

A
  • nuclear exosomes
  • cytosolic exosomes
79
Q

What is the function of nuclear exosomes?

A

degrade improperly modified RNA in the nucleus

80
Q

What is the function of cytosolic exosomes

A

target defective mRNA in the cytoplasm for degradation

Human Genomics & Genetics (7 decks)

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