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Mol / Cel Biology > Lecture 5 > Flashcards

Lecture 5 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Epigenetic pathways regulate?

A

Gene activity in a heritable manner without changing the primary nucleotide sequence of DNA.

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2
Q

Epigenetics structure changes are?

A

Changes are stable and reversible.

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3
Q

Crucial epigenetic reprogramming events occurs?

A

During germ cell development and early embryogenesis.

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4
Q

What is epigenomics?

A

Epigenetic changes in the level of whole genome?

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5
Q

Epigenetic events in eukaryotic organisms provides?

A

A more precise and stable control of gene expression and genomic regulation.

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6
Q

Epigenetic traits have a crucial role in?

A

Genomic stability.

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7
Q

What is the environmental epigenetic signal considered as? The one that triggers changes of the cell.

A

Epigenator.

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8
Q

Epigenator will lead to?

A

Activation of initiator.

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9
Q

Epigenetic initiator identifies?

A

Location on a chromosome where epigenetic marks will be established.

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10
Q

Initiator is xxx binding xxx?

A

Initiator is DNA binding proteins, non coding RNAs.

They are DNA sequence specific.

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11
Q

The ability of DNA-binding proteins to bind to specific

DNA sequences commonly results from?

A

Interactions between an α-helix in the DNA-binding

protein domain.

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12
Q

What is ncRNA?

A

Non-coding RNA. Functional RNA molecule
that is transcribed from DNA but not translated into
proteins

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13
Q

Epigenetic related non-coding RNAs are?

A

Short ncRNA

Long ncRNA

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14
Q

What is ncRNAs function?

A

To regulate gene expression at the transcriptional and post-transcriptional level

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15
Q

Short ncRNA -> microRNA. What does microRNA do?

A

Binds to a specific target mRNA with a complementary sequence to induce:
cleavage
degradation
block translation in the context of a feedback mechanismthat involves chromosome methylation

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16
Q

LongRNAs function?

A

Forms complex with chromatin modifying proteins and recruit their catalytic activity to specific sites in the genome

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17
Q

LongRNAs result after the modification and recruition?

A

Modification of chromatin state and influenced

gene expression.

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18
Q

What is DNA methylation?

A

Addition of a methyl group to the 5-carbon of the base cytosine in CpG-islands.

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19
Q

CpG sites are methylated by?

A

One of three enzymes called DNA methyl transferas (DNMTs)

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20
Q

DNA methylation of a gene’s CpG island repress?

A

Gene expression.

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21
Q

Non-CpG cytosine methylation has been identified at a high level in?

A

Stem cells. The loss of this form of methylation may

be critical in the differentiation.

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22
Q

Histone modification is a covalent what?

A

Covalent post-translation modification (PTM) to histone proteins

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23
Q

Which combination affects gene expression, DNA repair, and chromosome condensation?

A

PTM working together regulating the chromatin structure.

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24
Q

Histone protein PTM includes (5)?:

A 
Methylation
Phosphorylation
Acetylation
Ubiquitylation
Sumoylation
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25
Q

Histones structure?

A

Histone core and a loosely structured N-tail, which protrudes out of the nucleosome.

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26
Q

The majority of histones post-translational modification occurs at?

A

N-terminal tail.
Due to their chemical properties, these epigenetic
modifications alter the condensation of the chromatin and, as a consequence, the accessibility of the DNA to the transcriptional machinery.

27
Q

Histones can be acetylated on?

A

Lysine (K) residues. Enzymes regulating histone acetylation consist of the histone acetyltransferases (HATs) and histone deacetylases (HDACs).

28
Q

What does the acetyl groups addition does?

A

It neutralizes the positive charge of the amino group of the lysine.
Leads to decreased affinity between histone tail and negatively charged DNA

29
Q

Histone methylation occurs on?

A

Both lysine and argenine (R) residues.

This epigenetic modification is associated with both transcribed and silenced genes.

30
Q

Enzymatically, histone methylation is controlled by?

A 
Histone methyltransferase (HMTs) as well as by histone
demethylases (HDMs)
31
Q

Histone phosphorylation occurs on?

A

Serine (S), threonine (T) and tyrosine (Y) residues.
It is most commonly associated with transcriptional activiation.
Because Phos and DNA are both negatively charged.

32
Q

Ubiquitination refers to the attachment of?

A

The 72-amino acid protein ubiquitin to the histone core proteins H2A and H2B.
H2A ubiquitination is repressive.
H2B is active and repressed genes.

33
Q

Sumoylation - SUMO proteins are?

A

Roughly 100 amino acids long and added to their targets by specific ligases.

34
Q

Histone sumoylation is a mark of?

A

Transcriptional repression

35
Q

Acetyl - > Activation

SUMO -> Repression

A

;)

36
Q

Histone variants affects functionally what?

A

Chromatin remodelling and histone post-translational modifications.

37
Q

What does nucleosome remodelling refers to?

A

To the change in the structure of chromatin. The process requires ATP energy imput.

38
Q

Nucleosome remodelling is carried out by?

A

Enzymes called ATPase’s

39
Q

ATPpase’s activation can lead to?

A

Dissambly of nucleosomes.
Exchange of histones for variants.
Assembly of nucleosomes.

40
Q

What does allelic imbalance means?

A

The ratio of gene expression levels from each of two alleles in diploid genome is not 1 : 1

41
Q

Why does this allelic imbalance occurs?

A

Because variants in the DNA sequence causes different level of expression at two gene copies

42
Q

What the heck is monoallelic expression?

A

Only one of the two copies of a

gene is active, while the other is silent.

43
Q

Monoallelic expression has how many types?

A 
Four.
Somatic rearrangement.
Random allelic silencing or activation.
Genomic imprinting.
X chromosome inactivation
44
Q

In cancer tissues, DNA methylation is reduced or increased?

A

Reduced. Hypomethylating oncogene promoters, reducing defence against repetitive sequences leading to genome instability
and chromosome structural changes.

Decreased gene methylation has subsequent effects on
transcription.

45
Q

Somatic rearrangement in monoallelic expression?

A

Changes in DNA organization to produce functional gene at one gene copy, but not other.
Random choice of one gene copy.

46
Q

Random allelic silencing or activation in monoallelic expression?

A

Expression from only one gene copy at chromosomal localization (locus), due to different epigenetic changes.

Random choice of one gene copy. Specific cell type.

47
Q

Genomic imprinting in monoallelic expression?

A

Epigenetic silencing of gene copy in imprinted regions.

Imprinted region marked epigenetically according to the parental origin (parent-of-origin mechanism)

48
Q

X chromosome inactivation in monoallelic expression?

A

Epigenetic silencing of X chromosome linked genes on one female chromosome.

Random choice of C chromosome.

49
Q

What does epigenetics study?

A

How DNA interacts with smaller molecules found within cells, which can active or deactivate genes.

50
Q

In a nutshell what epigenetics can do?

A

Epigenetic changes can boost or interfere with the trascription of spesific genes.

51
Q

DNA or protein that’s wrapped around gets labelled with small chemical tags.
The set of all chemical tags that are attached to the genome in a given cell is called?

A

Epigenome.

52
Q

What does example the methyl group do to the gene?

A

It inhibits gene expression by interfering the transcription machinery
or causing the DNA to coil more tightly, making it inaccessible.

53
Q

Why can epigenetic changes can affect an organism for rest of its life?

A

Because epigenetic changes can survive cell division.

54
Q

Environmental factors can affect epigenetics, why?

A

Because the chemical tags that turn genes on and off can be influenced by factors like diet, chemical exposure and medication etc.

55
Q

Example: when skin cells divide, why they are still skin cells?

A

Epigenetics maintain their tissue identity.

56
Q

Tissue identity depends on?

A

Which genes are turned on and off.

57
Q

Acetylation of amino acids on histones generally correlates to gene activation. Why?

A

Acetylation reduces the positive charge of histone tails and repels the from the negatively charged DNA backbone in the packed nucleosome.

58
Q

Lysine and arginine amino acid residues on histone tails can be methylated. Methylation is more complex than acetylation.
Its correlation to gene activity depends on?

A

The context of where the mark is placed.

59
Q

Epigenetic regulation is established and maintained by how many classes of proteins or enzymes?

A

Three classes.

Readers, writers and erasers.

60
Q

Readers can?

A

bind either active or repressive marks on chromatin

61
Q

Writers can?

A

Place either active or repressive marks on chromatin

62
Q

Erasers can?

A

Remove marks from chromatin.

63
Q

What does initiator translate?

A

The epigenator signal

Mol / Cel Biology (17 decks)

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