Ch. 10 Nucleosomes, Chromatin, and Chromosome Structure

Question 1

Why do eukaryotic chromosomes need more compaction that prokaryotic chomosomes?

Answer 1

They are generally larger than prokaryotic chromosomes

Question 2

What does the compaction of a chromosome cause?

Answer 2

Causes DNA to become inaccessible to proteins. Replication and transcription will be inhibited.

Question 3

Do eukaryotic chromosomes remain compacted at the same level throughout the cell cycle?

Answer 3

No. Cells need to quickly condense and de-condense chromosomes during different stages of the cell cycle.

Question 4

What scale(s) will changes in compaction occur at?

Answer 4

Compaction changes can be on a global scale (entire chromosome) or local scale (regions of chromosome).

Question 5

What is chromatin?

Answer 5

chromosome (DNA) and any proteins bound to the DNA

Question 6

What are the most common proteins bound to DNA?

Answer 6

histones

Question 7

What is a nucleosome?

Answer 7

The structure formed when DNA wraps around histones. (“beads on a string”)

Question 8

Does compaction stop with nucleosomes?

Answer 8

No. Nucleosomes can be further packaged into higher order structures.

Question 9

What is the histone structure?

Answer 9

They are octamers made of four pairs of subunits that associate IN THE PRESENCE of DNA.
(2x H2A, 2x H2B, 2x H3, 2x H4)

Question 10

What are histone tails?

Answer 10

The N-terminus of histone subunits that protrude out from the histone.

Question 11

What do histone tails do/allow?

Answer 11

They allow adjacent nucleosomes to interact and further compact a chromosome (30nm fiber).

Question 12

What is a 30nm fiber?

Answer 12

The structure formed when nucleosomes are drawn together.

Question 13

What is involved in forming the 30nm fiber and how? (2)

Answer 13

1. H1(kind of like a clip) binds nucleosomes and creates higher order structure of a chromosome
2. Histone tails serve as contact points between nucleosomes

Question 14

What are loops and coils?

Answer 14

The structure formed when 30nm fibers are further arranged/condensed.

Question 15

What is the purpose of loops and coils?

Answer 15

They anchor to chromosomal scaffold proteins.

Question 16

Are there more levels of compaction beyond loops and coils?

Answer 16

Probably, but we are not sure as its not well understood. Several models exist, but there is NO universal explanation.

Question 17

At what organizational level might specifics of chromosomal compaction differ? (4)

Not DNA specifically, but levels of complexity

Answer 17

Species to species
Cell to cell
Chromosome to chromosome
Stage of the cell cycle

Question 18

How are bacterial chromosomes generally described? (3)

Answer 18

Prokaryotic chromosomes are generally smaller and NOT contained in a nucleus. They occupy most of the cell’s volume.

Question 19

Are SMC proteins found in prokaryotic cells?

Answer 19

Yes. They are involved in forming loop domains.

Question 20

Why might bacteria have less organization complexity? (2)

Answer 20

Less organization complexity may be related to the fast replication times and need to adjust to the environment quickly.

Question 21

How can chromosome structure be regulated? (2)

Answer 21

nucleosomes and enzymes

Question 22

How do nucleosomes regulate chromosome strucure?

Answer 22

They control accessibility of DNA to proteins like pol and transcriptional regulatory proteins.

Reduced compaction = greater accessibility
Increased compaction = lower accessibility

Question 23

What are the enzymes that facilitate/regulate chromosome structure changes? (2)

Answer 23

Chromatin remodeling complexes and Histone modifying enzymes.

Question 24

Where do the proteins involved in chromosome structure regulation exist?

Answer 24

They typically exist in complexes with transcriptional regulatory proteins.

Question 25

How can nucleosome arrangements be modified? (3)

Answer 25

Remodeling enzymes can reposition, remove, or replace histones.

Question 26

How can histones themselves be modified? What are the two types?

Answer 26

Chemical groups. 1. cis: directly affect the nucleosome 2. trans: attract proteins that affect the nucleosome

Question 27

What effect does modifying the nucleosome arrangement have on compaction?

Answer 27

It will "loosen" the DNA

Question 28

How can histone variants be produced?

Answer 28

Standard histone subunits can be substituted with variants that have different properties to allow a relaxed structure

Question 29

What are some possible effects of histone variants? (3)

Answer 29

lower affinity for DNA greater susceptibility to histone modifications varied protein recruitment

Question 30

How can histone tails be modified? (5)

Answer 30

acetylation of lysine methylation of lysine methylation of arginine phosphorylation of serine ubiquitination of lysine

Question 31

What do histone modifications cause in nucleosomes (2)

Answer 31

Some will open nucleosomes while others close nucleosomes.

Question 32

How does epigenetics pertain to histone modifications?

Answer 32

Histone modifications can be passed to daughter cells during mitosis or meiosis.

Question 33

How are epigenetic effects of histone modifications inherited?

Answer 33

Modifications may activate certain genes or repress certain genes. Inheritance of regulation patters of a gene can occur just like the inheritance of an allele occurs. (different from Mendelian inheritance bcs. DNA sequence isn't changing, the nucleosome structure is changing)

Question 34

How can histone modifications/epigenetics define which genes are expressed in daughter cells?

Answer 34

If the portions of a chromosome that are compacted remain compacted in the daughter cell, those genes won't be expressed.

Question 35

What do epigenetic modifications influence? (3)

Answer 35

development maintenance of tissue types (liver vs muscle) imprinting (silencing) of genes in germ cells

Question 36

How else can epigenetic marks be influenced? (1)

Answer 36

Some epigenetic marks can be influenced by environmental factors and lead to disease when the marks are disrupted. (i.e. stress, infectious agents...)

Question 37

What must be preserved for a cell to inherit chromosome structure?

Answer 37

histone modification patterns must be preserved during DNA replication

Question 38

How are histone patterns preserved during DNA replication? (5)

Answer 38

1. marked histones are present in parent DNA 2. histone octamers are split between strands during replication; each parent strand will still have some marked H3/H4 tetramers (H2A/H2B kicked out) 3. new unmarked H3/H4 tetramers will assemble and bind to the newly synthesized strand at histone binding sites 4. previously marked H2A/H2B dimers associate with the marked and unmarked H3/H4 tetramers on DNA 5. new H2A/H2B dimers will associate with the remaining H3/H4 tetramers (aren't enough marked)

Question 39

What is the result of this histone pattern preservation mechanism?

Answer 39

You get various combinations of marked and unmarked histones in nucleosomes.

Question 40

If some nucleosomes are fully marked, some are partially marked, and others are fully unmarked how is histone pattern conserved?

Answer 40

Presence of some fully marked nucleosomes attracts modification enzymes to that general area of the chromosome. These enzymes will fully mark and partially marked or fully unmarked nucleosomes.

Question 41

Describe the preservation of histone modification generally.

Answer 41

Modified parent histones lead to the modification of histones in the same region of newly synthesized DNA, resulting in the preservation of histone modification.