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Molecular Biology > Regulation Of Gene Expeession In Eukaryotes > Flashcards

Regulation Of Gene Expeession In Eukaryotes Flashcards

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1
Q

Why regulate gene expression?

A
  1. Control the types and quantities of proteins (gene products) produced
  2. Respond to the environment by turning on or off specific genes or groups of genes
  3. Turn genes on or off in the correct sequence during development
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2
Q

What are the 6 main steps involved in the regulation of gene expression in eukaryotes?

A
  1. Transcriptional control
  2. mRNA processing
  3. mRNA transport
  4. mRNA stability
  5. Ribosomal secretion
  6. Protein stability
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3
Q

Control of differential gene transcription involves:

A
  1. Cis-regulatory sequence of DNA (promoter and enhancer sequences
  2. Transcription factors (=trans-acting factors)- nuclear proteins that bind to promoter or enhancer sequences of genes and stimulate/ inhibit transcription
  3. Changes of chromatin conformation-
    - Gene methylation
    - Histine acetylation
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4
Q

Define epigenetics

A

A change in the expression of a gene that changes the phenotype without permanently changing the gene itself. Typically involving changes in chromatin structure

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5
Q

Describe epigenetics

A

Turning off expression without changing the code

Gene activity can be modulated in a manner that doesn’t involve changes in the DNA code and these changes can persist through one or more generations. These are called epigenetics effetcs

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6
Q

What are some examples of epigenetics?

A

Chromatin modifications

DNA methylation: can lead to parent-of-origin effects(imprinting which is not covered here)

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7
Q

What are the types of chromatin?

A

Euchromatin-are loose because they’re transcribed

Heterochromatin- dense packing if DNA, which makes it less accessible

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8
Q

What is nucleosome structure?

A

Positively charged histone proteins bind with each other along with DNA to form a structure called the nucleosome

The nucleosome core is composed of two molecules each of H2A, H2B, H3, and H4 histone proteins

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9
Q

What are nucleosomes connected by?

A

Linker DNA of variable length and H1 histone

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10
Q

How is the 30 Nm fiber formed from beads on a string?

A

Nucleosome can associate with each other via interactions between H1 to form a more compact structure that has been termed, due to size, the 30nm fiber

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11
Q

What are the two types of chromatin?

A

These are based on chromosome staining properties

Euchromatin-decondensed and transcriptionally active

Heterochromatin- condensed and transcriptionally inactive

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12
Q

What is the order of condensation of chromatin?

A
  1. DNA double helix-2nm
  2. Beads on a string- 11nm
  3. Chromatin fiber of packed nucleosomes- 30nm
  4. Extended section of chromosomes- 300nm
  5. Condensed section of chromosomes- 700 Nm
  6. Metaphase chromosomes
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13
Q

Give examples of histone modification that alter interaction of the DNA and the histone tails

A

Modifications include:

  • (de)acetylation
  • methylation
  • phosphorylation
  • ubiquitination (protein is destroyed in the proteosome “meat grinder”)
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14
Q

What enzymes are responsible for acetylation and deacetylation?

A

Acetylation by HATs(histone Acetyl transferase)

Deacetylation by HDACs (histone deacetylase)

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15
Q

Deacetylation is linked to…

A

Methylation of cytosine

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16
Q

Explain DNA methylation

A

DNA methylation involves the modification of the DNA base cytosine to 5-methyl-cytosine

DNA methyltransferase enzyme

Flag for silencing mechanism

17
Q

Explain methylation inheritance and transcriptional repression

A

Dnmt3-performs de novo methylation of DNA at cytosine

MeCP2- recruited to methylated cytosines (CpG islands)

HDAC 1 or 2- and other enzymes bind to MeCP2

Deacetylase activity (HDAC) on the acetylated lysine residues of the his robes leading to tightly packed chromatin

At DNA replication the full methylation pattern is restored. First, MeCP2 in an altered confirmation will recognize hemi-methylated DNA. This altered conformation of MeCP2 will recruit Dnmt1 which is also called the maintenance methyltransferase because it maintains the original methylation pattern

After DNA replication, there is conformational change of MeCP2. Again, HDAC 1 or 2 and other enzymes bind to MeCP2

Transcriptional repression is restored

18
Q

What are the enzymes involved in methylation inheritance and transcriptional repression?

A

Transcriptional repression and chromatin integrity
Dnmt3: DNA methyltransferase (de novo)

MeCP2: methyl CpG binding protein

Dnmt1: maintenance

19
Q

What kind of chromatin does transcription factor bind to?

A

Euchromatin is transcriptionally active, able to bind transcription factors and RNA polymerase

20
Q

What is the function of basal machinery?

A

Maintains low level of of transcription

Modulation requires more players

21
Q

What is the function of enhancer?

A

Retains function even when reversed or moved far from gene whose transcription it influences

22
Q

Where is the promoter?

A

Is close to a gene’s initiation site

23
Q

Regulation of gene transcription in eukaryotes involves the interaction of…

A
  • Basal transcriptional machinery located at the genes promoter
  • trans-acting proteins bound to did-regulatory elements
24
Q

Describe Cis-acting elements

A
  • contain short consensus sequences.
  • not fixed in location but usually within 200 bp upstream of the transcription start site
  • a single element is Usually sufficient to confer a regulatory response
  • can be located in a promoter or an enhancer
  • a specific protein binds to the element and the presence of that protein is regulated
25
Q

Describe trans acting elements

A
  • proteins that bind to the cis-acting sequences to control gene expression
  • Also called activator proteins and silencer proteins
  • Bind to promoter, enhancer, and silencer DNA in specific ways
  • Interact with other proteins to activate and increase transcription as much as 100-fold above basal levels
    - Or repress transcription in the case of silencers of repressors
26
Q

What are the common structural types of transcription factors?(dimer types)

A
  1. Zinc finger
  2. Helix-turn-helix
  3. Leucine zipper
27
Q

Folding of DNA can result in interactions between…

A

Enhancer or repressor proteins

Bound to distant cis-elements and the basal transcriptional machinery

Multiple sets of gene regulatory proteins can work together to influence transcription initiation

28
Q

Different genes provide the same cisxregulatiry sequences…

A

This provides spatial and temporal coordination of gene regulation

  1. Stage specific expression during embryonic development
  2. Tissue specific expression
  3. Response to external stimuli: hypoxia, hormonal, stress, heat
29
Q

Why are there 2 proline residues in HIF-a?

A

For hydroxylation by prolyl hydroxylase in normal oxygen environment

Ubiquitin ligase senders ligase, proteosome degrades HIF-a

30
Q

What happens to HIF-a in low oxygen environments?

A

Low oxygen environment causes HIF- 1a stabilization and transport nucleus where it binds to Hypoxia response element

While interacting with basal transcription machinery

Erythropoiesis, angiogenesis and anaerobic metabolism is stimulated

31
Q

Explain glucocorticoid response element

A

Glucocorticoid-steroid hormone

In the absence of glucocorticoid, the GR is maintained predominantly in the cytoplasm as part of an inactive multi protein complex

When glucocorticoid binds to GR, the receptor undergoes a change in conformation dissociates from regulatory heat shock proteins, and is hyperphosphorylated and moves to the nucleus

In the nucleus, hormone-activated GR regulates transcription. The GR binds as a homodimer directly to DNA sequences located in the promoter regions of glucocorticoid responsive genes. Binding to these sequences, known as glucocorticoid response elements

Leads to transcriptional induction or repression of target genes

32
Q

What are the types of glucocorticoid receptors?

A

These response elements are palindromic

There are positive GREs(trans activation ) and negative(transrepression) GREs

Molecular Biology (24 decks)

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