I . DNA & RNA | 2. Condensation levels of DNA in the eukaryotic cells; the role of topoisomerases and chromatin proteins Flashcards
Levels of chromosome condensation
(euchromatin, heterochromatin)
What is chromatin?
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.
The role of histones
to condensate the DNA
2 Types of chromatin
- Euchromatin
- Active transcriptionally
- Loosely packed - Heterochromatin
- Inactive transcriptionally
- Closely packed
Characteristics of euchromatin
- Active transcriptionally
- Loosely packed
Characteristics of heterochromatin
- Inactive transcriptionally
- Closely packed
Facultative: can transform into euchromatin
Constitutive: cannot serve as a template for transcription
2 types of heterochromatin
Facultative: can transform into euchromatin
Constitutive: cannot serve as a template for transcription
What are chromosome territories
specific territories in nucleus
Chromosome territories
- Inactive (condensed) segments are attached to ____
the nuclear periphery
Chromosome territories
- Transcriptionally active regions form loops, which hang into ___
more centrally positioned transcriptional ‘’factories’’
What is DNA condensation?
Refers to the process of compacting DNA molecules
_____ is a packed form of the DNA
Chromatin
During mitosis and meiosis, modification of the chromatin is called _____.
condensation
Packaging of eukaryotic DNA in chromatin
-> What are the 5 levels of DNA condensation?
- DNA double helix
- DNA wrapped around histone (beads on a string)
- Solenoid coil
- Radial loops
- Duplicated chromosome (metaphase chromosome)
Chromatin condensation is subject to ____ (which type of regulation?)
dynamic regulation
What are Nucleosomes?
fundamental unit of chromatin
What are Histones?
Histones, the most abundant in chromatin, are beads of proteins that binds DNA at a regularly space proteins
Structures of Nucleosomes
- 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
The role of Histone 1 (H1)
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
Describe solenoid structure
- 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
- These 2 strands are the wound into a left-handed double helix called a “two-start” helix
- The 30nm fiber also include H1 histone which is bound as it enters and exits the nucleosome core
- 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.
Describe Radical loops
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
What are Topoizomers?
Same DNA of different linking number
The role of type II topoisomerase: The DNA girase
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
How does type II topoisomerase: The DNA girase work?
- negative superhelical turns
- ATP-dependent helix unwinding by helicase generates positive superhelical turns, i.e., writhing.
- Girase is a type II topoisomerase, which cuts both DNA strands.
- It moves a distant section of DNA through the opening.
- Restores the continuity of the strands on the expense of ATP.
- By this, it regenerates negative superhelical turns.
The role of Type I topoisomerases
Type I topoisomerases cut one DNA strand only
How does Type I topoisomerases work?
- 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)
Further chromatin condensation is elicited by ___ and ___
histone H1
and a set of non-histone proteins (HMG + SMC)
