I . DNA & RNA | 2. Condensation levels of DNA in the eukaryotic cells; the role of topoisomerases and chromatin proteins

Question 1

Levels of chromosome condensation
(euchromatin, heterochromatin)

Answer 1

Question 2

What is chromatin?

Answer 2

Chromatin consists of very long double stranded DNA molecules and a nearly equal mass of rather small basic proteins termed histones, as well as a smaller amount of non-histone proteins.

Question 3

The role of histones

Answer 3

to condensate the DNA

Question 4

2 Types of chromatin

Answer 4

1. Euchromatin
   - Active transcriptionally
   - Loosely packed
2. Heterochromatin
   - Inactive transcriptionally
   - Closely packed

Question 5

Characteristics of euchromatin

Answer 5

• Active transcriptionally
• Loosely packed

Question 6

Characteristics of heterochromatin

Answer 6

• Inactive transcriptionally
• Closely packed
   Facultative: can transform into euchromatin
   Constitutive: cannot serve as a template for transcription

Question 7

2 types of heterochromatin

Answer 7

 Facultative: can transform into euchromatin
 Constitutive: cannot serve as a template for transcription

Question 8

What are chromosome territories

Answer 8

specific territories in nucleus

Question 9

Chromosome territories
- Inactive (condensed) segments are attached to ____

Answer 9

the nuclear periphery

Question 10

Chromosome territories
- Transcriptionally active regions form loops, which hang into ___

Answer 10

more centrally positioned transcriptional ‘’factories’’

Question 11

What is DNA condensation?

Answer 11

Refers to the process of compacting DNA molecules

Question 12

_____ is a packed form of the DNA

Answer 12

Chromatin

Question 13

During mitosis and meiosis, modification of the chromatin is called _____.

Answer 13

condensation

Question 14

Packaging of eukaryotic DNA in chromatin
-> What are the 5 levels of DNA condensation?

Answer 14

1. DNA double helix
2. DNA wrapped around histone (beads on a string)
3. Solenoid coil
4. Radial loops
5. Duplicated chromosome (metaphase chromosome)

Question 15

Chromatin condensation is subject to ____ (which type of regulation?)

Answer 15

dynamic regulation

Question 16

What are Nucleosomes?

Answer 16

fundamental unit of chromatin

Question 17

What are Histones?

Answer 17

Histones, the most abundant in chromatin, are beads of proteins that binds DNA at a regularly space proteins

Question 18

Structures of Nucleosomes

Answer 18

• They are ‘’beads-on-a-string’’ arrangement of histone and DNA together
• The bead of each nucleosome contains eight ‘’core’’ histone molecules (octamer), 2 copies of each H2A, H2B, H3 and H4
  +) High lysine/arginine content,
  positively charged proteins ->
  electrostatic interactions with negatively charged DNA
  +) HISTONE ACETYLTRASNFERASE

Question 19

The role of Histone 1 (H1)

Answer 19

Further chromatin condensation is elicited by histone H1
and a set of non-histone proteins (HMG + SMC)

Histone H1 binds to linker DNA between nucleosome beads

Question 20

Describe solenoid structure

Answer 20

1. The 30 nm fiber has a “zig-zag ribbon structure” of nucleosomes containing 2 “strands.” In each “strands,” the nucleosomes are aligned with each other like a stack of coins
2. These 2 strands are the wound into a left-handed double helix called a “two-start” helix
3. The 30nm fiber also include H1 histone which is bound as it enters and exits the nucleosome core
4. Organization into 30nm fibers does not extend over the entire chromosome but is punctuated by regions bound by sequence-specific (non-histone) DNA- binding proteins.

Question 21

Describe Radical loops

Answer 21

In long loop of chromatin, 30nm fiber is associated with a protein scaffold made up in part of structure maintenance of chromosome (SMC) proteins at sites between transcription unit
- Scaffold-anchored regions (SARs) or matrix-anchored regions (MARs) are located at the base of DNA loops
- Loops of chromatin are also found to be tethered at the base by SMC complexes which have ATPase activity at the head domain (the 2 monomers of SMC complex are also linked by kleisin protein)
+) Each SMC complex linked 2 chromatin fibers

Question 22

What are Topoizomers?

Answer 22

Same DNA of different linking number

Question 23

The role of type II topoisomerase: The DNA girase

Answer 23

Girase is a type II topoisomerase
- Make breaks in both strands of a double-stranded DNA and then religates them
=> Relieving torsional stress and linking together 2 circular DNA molecules as in the link of the chain

Question 24

How does type II topoisomerase: The DNA girase work?

Answer 24

1. negative superhelical turns
2. ATP-dependent helix unwinding by helicase generates positive superhelical turns, i.e., writhing.
3. Girase is a type II topoisomerase, which cuts both DNA strands.
4. It moves a distant section of DNA through the opening.
5. Restores the continuity of the strands on the expense of ATP.
6. By this, it regenerates negative superhelical turns.

Question 25

The role of Type I topoisomerases

Answer 25

Type I topoisomerases cut one DNA strand only

Question 26

How does Type I topoisomerases work?

Answer 26

• Binds to DNA at random sites and breaks a phosphodiester bond in 1 strand
  -> Such a one-strand break is called a nick
• The broken end then unwinds around the uncut strand, leading to loss of supercoils
• Finally, the same enzyme joins (ligates) the 2 ends of the broken strand.

(Role: To relieve the torsional stress that develops in cellular DNA molecules during replication or other processes)

Question 27

Further chromatin condensation is elicited by ___ and ___

Answer 27

histone H1
and a set of non-histone proteins (HMG + SMC)