Eukaryotic gene regulation

Question 1

Gene regulation is?

Answer 1

Gene regulation is the process of turning genes on and off

Question 2

Gene expression is?

Answer 2

Gene expression is the process by which the instructions in our DNA are converted into a functional product, such as a protein

Question 3

What are the signals for the gene regulation?

Answer 3

1. Internal signals: come from inside the cell
   DNA functioning properly or any damage (organelles), amount of ATP the cell has (inside the cells of the body).
2. External signals: come from outside the cell
   - messages from other cells (growth factors), environmental stimuli (nutrients availability), pH and temperature etc.

Question 4

What are the 3 stages of Signal Transduction Pathway?

Describe each in own words.

Answer 4

1) Reception - Growth factors (proteins from another cell) bind to receptors on the plasma membrane
2) Transduction - Signal transduction pathway (the whole process) triggers activation of transcription factors (molecules - signal transducers also affect each other going down). Signal transducers pass the signal from the cell membrane to the transcription factors (activating it).
3) Response - Transcription factors target a particular gene, so that genes (some particular genes from DNA) can be transcribed and translated; and the protein will be produced.
Proteins produced stimulate cell division (the part of the response in this case, but not in all examples)

Question 5

Which changes transcription requires in chromatin structure? (Chromatin Remodeling Complexes) in own words

Answer 5

a group of proteins bind to the DNA (in the chromatin) and change the structure of the chromatin (to expose the promoter). Promoters of inactive genes are hidden in nucleosomes. To activate a gene, transcription factors (proteins) bind to enhancers (DNA sequence) and attract chromatin remodeling proteins. The chromatin remodeling proteins: 1. change the location of nucleosomes 2. remove histones from the DNA; 3. replace core histones with variants (coactivators). As a result, the promoter (the sequence of DNA) becomes more accessible, so that RNA polymerase II can bind to the promoter and transcription can occur.

Question 6

What are the functions chromatin remodeling proteins?

Answer 6

1. change the location of nucleosomes
2. remove histones from the DNA
3. replace core histones with variants (coactivators)

Question 7

What will happen when we add methyl group to the tails of histone proteins?

Answer 7

This brings either the activation or repression of transcription, depending on which amino acid tail we have.

Question 8

What is the acetylation?

Answer 8

Acetylation is the addition of acetyl groups (CH3CO) to histone proteins.

Question 9

What is DNA methylation and how it occurs??

Answer 9

5 methylcytosine (cytosine base pair is usually methylated, CH3 group is added), which occurs via DNA methyltransferase (enzyme, which transfer methyl group to the nitrogenous base in the DNA).

Question 10

Heavily methylated DNA VS Unmethylated

Answer 10

Heavily methylated DNA is associated with the _repression (inhibition) _ of transcription (transcriptionally inactive). This means that DNA is not available for transcription. Transcriptionally active DNA is usually unmethylated (DNA is available for transcription).

Question 11

What is proteome?

Answer 11

The complete number of proteins that a cell can make. Proteome is not directly related to the number of genes in the genome. (Because each gene can make different proteins).

Question 12

What are enhancers?

Answer 12

1. Enhancers: sequences of DNA, which are:

a. capable of affecting transcription at distinct promoters (different sites)

Question 13

How do enhancers affect transcription?

Answer 13

Transcriptional activator proteins always bind to the enhancer on the DNA. When transcriptional activator proteins (that come from enhancers) bind to the promoters, it stimulates transcription.

Question 14

How do enhancers affect transcription when so far away from promoters?

Answer 14

(Transcriptional) activator proteins bind to the enhancer (and then to the promoter) and cause the DNA between them (between the enhancer and the promoter) to loop out.

Question 15

What are insulators?

Answer 15

DNA sequences that block or insulate (isolate) the effect of enhancers based on the position on the DNA

Question 16

What if insulator is not between the enhancer and the promoter (located outside the region)

Answer 16

If insulator is not between the enhancer and the promoter ( meaning it’s outside the region) – it would have no effect on promoters
(so that loops would not be created). And transcription for both genes would occur, so that enhancer I would affect on gene A and gene B; and enhancer II would affect on gene B and gene A

Question 17

what happens if insulator lies between enhancer and promoter?

Answer 17

If insulator lies between enhancer and promoter- _it blocks (binding the activator protein from the enhancer to the other promoter, which prevents
transcription of the gene for promoter).

Question 18

What are the 2 types of Small Regulatory RNAs?

Answer 18

They are miRNAs and siRNAs.

Question 19

What are the 2 effects of miRNA binding to mRNA?

Answer 19

(1) if miRNA and its target mRNA match, an enzyme (miRNA protein complex, green enzyme) will chop the mRNA leading to its breakdown (destabilizing mRNAs - no translation).
(2) If miRNA and its target mRNA only partially match, the complex will bind to the mRNA and block (prevent) it from being translated.

Question 20

Proteins can be modified after translation. True or False? Provide an example

Answer 20

True. For example: removal of amino acid (change the protein activity), addition of chemical groups (determine how long the protein will function in the cell), proteins chopped, tagged for degradation (destruction of protein) etc. They determine how long the protein is going to be in the cell (to carry out it’s function) before it’s broken down.

Question 21

What is the Genomic Imprinting?

Answer 21

phenomenon in which the expression of a gene depends on whether it is inherited from the male or the female parent

Question 22

What is the monoallelic expression?

Answer 22

The expression of the gene, when one allele is epigenetically silenced - which means turned off for one parent. We can have the same inherited genotypes from parent, but different phenotypes.

Question 23

Maternally vs Paternally expressed growth

Answer 23

a. Maternally expressed (paternally imprinted - not expressed) genes (copy from mom is used) usually suppress growth
b. Paternally expressed (maternally imprinted - not expressed) genes usually enhance growth

Question 24

Explain in your own words what is the destabilization of the histones.

Answer 24

When we add the acetyl group, the histones become destabilized (unstable), which will lead to their displacement (replace). The nucleosome is stable. The histones must become unstable in order to displace (remove) them by the chromatin remodeling proteins, so that it allows transcription factors to get access to the promoter DNA (acetylation).

Question 25

How acetyl groups affect transcription?

Answer 25

Generally, acetyl groups destabilize (to make unstable) the chromatin structure allowing for transcription to occur.

Question 26

Transcription factors definition

Answer 26

Transcription factors are proteins (activators, enhancer, promoter, mediators) that interact directly through DNA binding and influence transcription.

Question 27

How can we activate the gene on promoter?

Answer 27

To activate a gene on the promoter, transcription factors (proteins) bind to enhancers and recruit chromatin remodeling proteins (so that coactivator displaces the histone proteins in the nucleosome).

Question 28

What is a promoter in eukaryotes? What it means that promoters are “hidden”

Answer 28

DNA sequences that act as signals to provide the exact location for the initiation of transcription (RNA polymerase II binds here).
When promoters are wrapped around histone proteins in the nucleosome, then the promoter DNA will not be accessible (means it can’t be used, because it’s already occupied around histones), therefore the genes are “hidden”.

Question 29

What is ATP, its function and where it is found?

Answer 29

ATP is the source of energy, which captures its chemical energy from the breakdown of food molecules (in the organism) and releases it to fuel other cellular processes.
ATP molecules synthesized in the mitochondria

Question 30

Acetylation vs Deacetylation

Answer 30

We remove histone proteins and add acetyl group to the histone tail in acetylation (DNA is available for transcription to occur) But, in deacetylation, we add histone proteins and remove acetyl group from the histone tail.
(DNA is not available for transcription to occur)

Question 31

What are the 2 types of destabilization methods of the histones?

Answer 31

The destabilization methods of the histone proteins are methylation (it depends on the amino acid tail) and acetylation (which doesn’t depend on the amino acid tail).

Question 32

Acetyltransferase VS deacetylases (enzymes)

Answer 32

Acetyltransferase enzymes add acetyl groups (acetylation), so that promoters become accessible (decondensed) and transcription can occur (most of the time).
Deacetylases enzymes strip (remove) acetyl groups (deacetylation), so that they can restore chromatin structure (condensed) and stop transcription.

Question 33

What is RNA (alternative) splicing?

Answer 33

Alternative splicing allows pre-mRNA (exons) to be spliced (cut and join in different site) in multiple ways, generating different proteins (by splicing repressors enzymes) from one gene (in the DNA).

Question 34

Provide examples of imprinting genes in humans both located within same region of chromosome 15

Answer 34

a. insulin growth factor 2 (IGF2) paternally derived, maternally imprinted
b. H19 gene maternally derived, paternally imprinted (silent on paternal)

Question 35

Describe example of a hypothetical gene for body color

Answer 35

• Maternally imprinted (paternally inherited turned on)
• The daughter passes that imprinted gene on from the father, but it is turned off in the grandchildren, since it’s now maternally inherited.

Question 36

What is TATA box?

Answer 36

TATA box is the sequence of DNA on the promoter region, which is recognized by the RNA polymerase and initiates the process of transcription