DNA Packaging (6)

Question 1

Are chromosomes wound or unwound when in a defined territory in interphase?

Answer 1

Unwound

Question 2

What holds c’somes in their territories?

Answer 2

nuclear matrix
Nuclear lamina

(both PRO frameworks)

Question 3

Where is heterochromatin located in the nucleus? & where is it attached

Answer 3

Periphery of the nucleus

attached to nuclear lamina

Question 4

Where is euchromatin located? & what does it contain?

Answer 4

toward interior of nucleus

where transcription machinery is located

Question 5

Why do c’somes overlap territories?

Answer 5

to share transcriptional machinery

Question 6

Nucleosomes

Answer 6

grp of positively charged highly conserved PROs

Question 7

How is DNA held by histones?

Answer 7

ionic bonds b/w negatively charged sugar phosphate backbone & positively charged histones

Question 8

What are the levels of organization of histones in DNA packaging?

Answer 8

o Level 1 10nm: histones, DNA wraps around nucleosome
o Level 2 30nm: assembly of adjacent nucleosomes
o Level 3 looped domains: MARs have an affinity for the scaffold
o Level 4 c’somes have looped domain structure

Question 9

Cohesin of looped domains

Answer 9

ring shaped PRO may contain loops

Question 10

Matrix Assoc Region

Answer 10

DNA sequence that has a high affinity for the nuclear matrix, DNA loop can be moved to facilitate transcription

Question 11

What is MAR composed of?

Answer 11

alpha satellite

non-coding DNA

Question 12

What is the function of MARs?

Answer 12

provides structure to DNA to anchor it to the PRO (no function provided)

Question 13

What is MAR’s role in initiating transcription?

Answer 13

Transcription is initiated by the RNA polymerase on the nuclear matrix by drawing the loop towards it

Question 14

What is a nuclear matrix & what are the major organizing structures?

Answer 14

PRO framework

o RNA polymerase (makes mRNA)
o RNA processing PRO
o DNA replication PRO

Question 15

Topoisomerase II

Answer 15

un-tangling PRO (for unwinding DNA for replication)

Question 16

Insulator PRO

Answer 16

keeps loops separate & enables transcription machinery to regulate separate loops at a time

Question 17

Nuclear lamina

Answer 17

lamins bind telomeres & alpha satellite DNA of the centromere

Question 18

How can the nuclear scaffold be viewed?

Answer 18

Digesting DNA & removing histones

Question 19

What are the 4 scaffold PROs?

Answer 19

nuclear matrix
topoisomerase II
insulator PROs
nuclear lamina

Question 20

What activates condensin?

Answer 20

phosphorylation by MPF

Question 21

Describe mitotic c’somes

Answer 21

• Have looped domain structure
o Chromosome in proper structure for replication
o No nucleus present when chromosomes are seen in this state
o DNA loops on condensin PRO
o More compact than interphase chromatin
o Condensin is activated by phosphorylation via MPF

Question 22

How does the cell make DNA accessible to PROs for transcription?

Answer 22

modifying histones

Question 23

What are the mechanisms of histone modification?

Answer 23

o Replacement with modified types of histone

o Chemical modification of the histones

Question 24

H2A.X

Answer 24

o ATM PRO must signal to the cell to get checkpoint going to stop mitosis from occurring when DNA is damaged
o Replaces H2A less than 10% of nucleosomes receptive for ATM PRO
o ATM phosphorylates a target … H2AX signaling where repair is necessary

Question 25

macroH2A

Answer 25

barr body –> keeps chromatin condensed & inactive

Question 26

What are the 3 chemical modifications of histones?

Answer 26

• Acetylated histones looser DNA binding
o Acetyl grp is negatively charged by weakening some of its own positive charge
Decreases the affinity for the positively charged DNA
o HAT adds acetyl grp onto histone & opp is down with HDAC (more condensed wrapping)
• Phosphorylated histones can increase or decrease DNA winding of histones
o Can weaken or tighten interaction b/w DNA & histones

Question 27

What are the 2 types of heterochromatin?

Answer 27

constitutive

facultative

Question 28

How does heterochromatin work?

Answer 28

covered in histones

making DNA unavailable to machinery

Question 29

Constitutive Heterochromatin & an ex

Answer 29

o condensed always
AT rich alpha satellite DNA at the centromere
Telomeres (ends of chromosomes)

Question 30

Facultative Heterochromatin

Answer 30

o transient condensation, contains temporary active genes
Can be condensed or opened
Signals sent when genes needed & it unwraps

Question 31

How does the X inactivation occur?

Answer 31

o XIST RNA accumulates along the chromosome & inactivates genes barr body

Question 32

barr body

Answer 32

highly condensed X c’some

Question 33

What events does XIST induce? & how?

Answer 33

Deacetylation of DNA of H3
Methylation of H3
Ubiquitination of H2A

How –> recruitment of enzymes