chromatin structure and histone code

Question 1

What is the first level of DNA packaging? [2 marks]

Answer 1

• DNA is packed into nucleosomes (associated with histones).

- This increases DNA packaging by 7 fold.

Question 2

What is the second level of DNA packaging? [2 marks]

Answer 2

• Nucleosomes pack themselves into 30nm long fibres.

- This increases packaging by 6 fold.

Question 3

What is the third level of DNA packaging? [2 marks]

Answer 3

• 30nm fibres pack themselves into 80-100nm fibres.

- This increases packaging by 3 fold.

Question 4

What is the fourth level of DNA packaging? [2 marks]

Answer 4

• This represented by the chromosome.

- This represents 10,000 fold packaging.

Question 5

What are chromosomes made out of? [4 marks]

Answer 5

• DNA
• Histone proteins
• Non-histone proteins
• Non coding RNA

Question 6

What is the structure of nucleosomes? [4 marks]

Answer 6

• Made up of 8 globular proteins. (“beads on a string”)
• Linker DNA outside
• DNA is wrapped around the outside of histones
• N terminal tails on the outside of the octamer core (positive charge)

Question 7

What are the histones preset in nucleosomes? [4 marks]

Answer 7

• 2 x H2A
• 2 x H2B
• 2 x H3
• 2 x H4

Question 8

Is DNA packed in the 3rd level functional or not? [1 mark]

Answer 8

NO

Question 9

What does the compaction of nucleosomes require? [2 marks]

Answer 9

• Linker histones

- Modification of histones

Question 10

Do nucleosomes need to be removed during transcription? [1 mark]

Answer 10

YES

Question 11

What are histone remodelling factors? [1 mark]

Answer 11

Enzymes that remove and replace nucleosomes.

Question 12

What does heterochromatin rich DNA look like? [3 marks]

Answer 12

• Dark when stained with Giemsa
• Gene poor
• Highly condensed (resistant to gene expression)

Question 13

What does euchromatin rich DNA look like? [3 marks]

Answer 13

• Light when stained with Giemsa
• Gene rich
• Loosely condensed

Question 14

What perecentage of the genome does heterochromatin rich genes make up and where are they found? [2 marks]

Answer 14

• ~10%

- Found near centromeres and telomeres

Question 15

What perecentage of the genome does euchromatin rich genes make up and where are they found? [2 marks]

Answer 15

• ~90%

- Found in active genes

Question 16

Where can facultative heterochromatin be found? [2 marks]

Answer 16

GLOBIN GENE

• present as euchromatin in reticulocytes.
• present as heterochromatin everywhere else.

Question 17

What are ways to determine how nucleosomes are packed? [2 marks]

Answer 17

• Acetylation of lysine residues in histone tails.

- Methylation of lysine and arginine residues.

Question 18

How do scaffolds protect DNA? [2 marks]

Answer 18

• They have insulators that insulate chromatin in one loop from the next.
• This prevents one set of genes from affecting another.

Question 19

What are DNAse I sensitive sites (HSS)? [2 marks]

Answer 19

• Places that are easily digested by DNAse I, even in chromatin form.
• Have a regulatory role; allow regulatory factors to get to them.

Question 20

What do transcription factors do to chromatin and how? [4 marks]

Answer 20

• They recruit chromatin modifying enzymes.
• This is via a nuclear coactivator (NCoA) or corepressor (NCoR).
• NCoA bind a bunch of enzymes (histone acetyl transferase and histone methyl transferase).
• This opens up the chromatin structure.

Question 21

How does acetylating histones work? [2 marks]

Answer 21

• Acetylated HAT acetylate amino group of lysine.

- Lysine loses its positive charge.

Question 22

Acetylation in heterochromatin and euchromatin [2 marks]

Answer 22

HETERO: unacetylated
EU: acetylated

Question 23

What happens to the thyroid hormone receptor without thyroid hormone? [2 marks]

Answer 23

• Thyroid hormone receptor binds NCoR which binds histone deacetylase (HDAC) and DNA Methylase.
• Chromatin is packed tightly.

Question 24

What happens to the thyroid hormone receptor in the presence of the thyroid hormone? [3 marks]

Answer 24

• When hormone binds to its receptor, there’s a change in confirmation.
• Receptor binds NCoA which recruits HAT and HMT.
• Histones are modified and chromatin is opened up.

Question 25

How can lysine be methylated? [3 marks]

Answer 25

• Monomethylated
• Dimethylated
• Trimethylated

Question 26

How are histone modifications read? [2 marks]

Answer 26

• By binding proteins

- Read multiple lysine residues and multiple modifications.

Question 27

What is the clinical significance of HDAC? [3 marks]

Answer 27

• HDAC inhibitors are used to activate genes.
• They keep them in an open configuration.
• HDAC affects gamma globin gene in sickle cell anaemia or cancers.