Gene Expression Control II

Question 1

How can packaging of DNA be loosened?

Answer 1

Aceylation, methylation, and phosphorylation.

Acetylation of the tails weakens their interaction with DNA and may permit some transcripion factors to bind to DNA.

Question 2

If DNA is packaged around nucleosomes, how does the transcription machinery as well as transcription factors attach to the DNA?

Answer 2

Transcription activators trigger changes in chromatin structure making DNA accessible.

Histones are modified and nucleosomes are remodelled.

Histone modification enzymes are important for this.

Question 3

What does acetylation do?

Answer 3

Acetylation neutralizes histones making them less attracted to the negative charge of DNA allowing to unwind to permit transcription.

Question 4

What is the histone code?

Answer 4

Set of modifications to histone proteins which governs how tightly they bind to DNA

Question 5

How is histone code maintain in the cell?

Answer 5

Parental patterns of modification are inherited in daughter chromosomes.

Question 6

How do we know that histones are a mix of old and new proteins?

Answer 6

Using isotopically-labelled histones.

Question 7

What is DNA’s charge?

Answer 7

Negative

Question 8

What is a histone protein’s charge?

Answer 8

Positive

Question 9

What proteins add or remove acetyl groups from histones?

Answer 9

Using histone acetylase and histone deacetylase

Question 10

How can histones be modified to allow for DNA transcription to take place?

Answer 10

Nucleosome sliding

Nucleosome removal creating nucleosome free DNA

Histone variants allow greater access to nucleosomal DNA

Specific patterns of histone modification destabilize compact forms of chromatin and attract components of transcription machinery

Question 11

How can histones be modified to allow for DNA transcription to take place?

Answer 11

Nucleosome sliding

Nucleosome removal creating nucleosome free DNA

Histone variants allow greater access to nucleosomal DNA

Specific patterns of histone modification destabilize compact forms of chromatin and attract components of transcription machinery

*all these modifications of histones can be done via chromatin remodeling complex

Question 12

For some genes, nucleosomes may need to be moved. How does this take place?

Answer 12

SWI-SNF is an ATP dependent chromatin remodelling protein that activates transcription by moving nucleosome away from the TATA box allowing initiation complex to form.

Question 13

What is SWI-SNF named after?

Answer 13

Switch & sugar non-fermenting mutants in yeast

Question 14

What does SWI-SNF do?

Answer 14

Has helicase activity which pushes DNA around nucleosomes

Binds to histones with acetylated tails

Remains bound and maintains region in decondensed conformation

Allows access of TFs and RNApol to TATA box.

Question 15

How is chromatin structure modified to alter gene transcription?

Answer 15

Modification of histone proteins (as mentioned before)

Chromatin remodeling

DNA methylation

Question 16

What are epigenetics?

Answer 16

Some chromatin structure changes are retained when cells divide and can even be inherited

Question 17

What are the mechanisms of epigenetics?

Answer 17

Histone modification

DNA methylation

Question 18

What is DNA methylation?

Answer 18

Common modification to the primary structure of DNA. Cytosine is commonly methylated to 5-methyl C and hypermethylation suppresses transcription.

Question 19

What does methylation do?

Answer 19

Condenses chromatin and represses transcription.

This process is reversed by demthylation

Question 20

What does the ‘p’ refer to in CpG?

Answer 20

The phosphodiester bond between cytosine and guanine

Question 21

What are CpG islands?

Answer 21

Many CpG arrangements in a row that are often methylated to suppress gene expression.

Question 22

How is RNA exported?

Answer 22

Export of RNA is delayed until processed completely and damaged RNA is degraded by exosomes/exonucleases

Question 23

How is RNA transported?

Answer 23

mRNAs are localised to specific regions in the cytosol. mRNA is met by ribosomes and translated.

Question 24

What information does mRNA carry about its own expression?

Answer 24

Half-life

Efficiency of translation

3’ untranslated region contains specific signals to direct transport

Question 25

How is mRNA translocation controlled?

Answer 25

mRNA travels along cytoskeleton and stopped by anchor proteins

Question 26

Why must mRNA be transported near where the protein it produces is required?

Answer 26

To ensure that the protein is produced at the right location.

Question 27

How is mRNA degradation controlled?

Answer 27

mRNA stability can modify half life between 30 minutes and 10 hours.

Shortening poly A tail by exonuclease when mRNA reaches cytosol. Poly A tail acts as a timer for mRNA.

Question 28

How is mRNA destroyed?

Answer 28

2 general mechanisms after poly A tail reaches 25 nucleotides:

5’ cap is removed degrading mRNA from 5’ end.

mRNA continues to be degraded from 3’ end

Question 29

What end of the mRNA is the poly A tail located?

Answer 29

3’

Question 30

What end is the cap located on mRNA?

Answer 30

5’

Question 31

How is mRNA translation controlled?

Answer 31

Control often exerted at initiation stage.

5’ cap important in binding small ribosomal subunit then finds AUG start site for translation.

3’-UTR is also important for translation initiation. Only when both ends of the mRNA are checked can translation take place

3’ and 5’ end must both bind simultaneously.

Question 32

How is translation not overdone? (how is mRNA not constantly translated without stopping?)

Answer 32

There is competition between mRNA translation and decay.

5’ cap and 3’ polyA tail are used in both translation initiation and deadenylation-dependent mRNA decay.