DLA 2-Chromosomal Organization Flashcards
Describe the enclosure of eukaryotic DNA
Eukaryotic DNA is isolated from the rest of the cell within a nuclear envelope called the nucleus
How much of the eukaryotic cell volume is taken up by the nucleus/eukaryotic DNA?
About 10% of cell volume
How much of the nucleus does the nucleolus occupy?
25% of the nucleolus
What is the purpose of the nucleolus?
Has central role making in making ribosomal RNA and ribosomal proteins
Detail the structure of the nuclear envelope
- is formed by lipid membranes
- contains large nuclear pores to transport molecules in and out
- Outer membrane also forms the endoplasmic reticulum
- nuclear lamina is fibrillation network that is associated with the inner membrane and provides stability
- heterochromatin is found near the lamina
What is heterochromatin?
Condensed DNA which is inactive, not being transcribed and is accessible to RNA polymerase
Chromosomes in interface are often referred to as _____________
Chromatin
What is euchromatin?
This is the active DNA , actively being transcribed into RNA and is accessible to RNA polymerase
Which is more abundant, heterochromatin or euchromatin ?
Most chromosomes are inactive in interphase, so heterochromatin is the most abundant
Where are chromosomes in interphase?
In interphase, they occupy chromosome territories.
List the general steps in how interphase DNA organize into the discrete chromosome structures for mitosis
- Formation of nucleosomes
- Formation of 30nm fiber
- Formation of 300nm fiber
- Condensed Chromosome 700nm
- Mitotic Chromosomes
What are histones?
Proteins which interact with chromatin
Name each histone protein
Various histone isoforms form an octamer
2 of each that form the octamer: (H2A, B , H3 and H4)
How are nucleosomes formed?
- DNA wraps twice around the octamer and thus is called a nucleosomes
- Nucleosomes have spacer DNA plus the H1 isoforms histone
- Can be refferred to as “beads on a string”
What is the Lysine-Arginine content and molecular weight of H1?
H1 is Lysine rich with a molecular weight of 23,000 Da(highest out of all histone isoforms)
What is the Lysine-Arginine content and Molecular weight of H2A histone protein ?
Slightly lysine-rich and molecular weight of 14,000 Da
What is the Lysine-Arginine content of the H2A protein and it’s molecular weight?
H2B is slightly Lysine rich and has a molecular weight of 13,800Da
What is the Lysine -Arginine content and molecular weight of H3?
H3 is Arginine rich with MW of 15,300
What is the Lysine-Arginine content and molecular weight of H4 histone isoforms ?
H4 is Arginine rich and molecular weight of 11,300
What is usually the positive charge of H3 and why?
H3 usually has a charge of +14, close interaction with the negatively charged DNA
Who performed x ray crystallography on the histone DNA nucleosome?
Richman and colleagues
How do histone tails affect the DNA helix?
- Histone tails protrude into the minor groves of the DNA helix
- Amino acids on the histone tails can be chemically modified to change how the tails interact with the DNA
Positively charged amino acids like Lysine can be acetylated, what effect does this have ?
Acetylation will interrupt ionic bonding between lysine and DNA, resulting in a more relaxed interaction
What are the most commonly phosphorylated amino acids?
Serine, threonine and tyrosine
What amino acids can be phosphorylated?
Serine, threonine and Tyrosine -most common
But also arginine, lysine, aspartic acid, glutamic acid and cysteine
What effect that some amino acids can be phosphorylated on the ability of positively charged histone tails to interact with negative charged DNA?
Phosphorylation of histone tails reduces the positive charges on the histone tail, can occur during particular times of the cell cycle such as mitosis which decreases the positive charge on histone tails
Describe the formation of 30 nm fiber
- beads on string formation will further condense to a 30 nm fiber
- H1 histones(purple) associate to form the core of the 30nm fiber, also referred to as the solenoid structure
What role did Robinson play in understanding the 30nm fiber formation?
Robinson and coworkers reconstituted 30 no fibers in vitro and performed X-ray crystallography to characterize the packaging of DNA
Describe the formation of 300 Na fiber
- the 30 nm fibers are folded into large loops of interphase chromatin
- Can be refferred to as “bottle brush” or “rosettes of chromatin loops”
- Non-histone proteins form a scaffold for the chromatin in the nuclear matrix
- the diameter of the chromatin fiber is now 300 nm
- this DNA can still be replicated or transcribed to RNA
How much base pairs are contained in each bottle brush/rosettes of chromosome loops/ loops in 300 no fibers?
Each loop contains between 20,000 to 80,000 base pairs
Can DNA in a 300 no fiver be replicated or transcribed to RNA?
Yes
Describe the formation of condensed chromosomes- 700 nm
Beginning in early mitotic cell cycle, the chromatin is in its most compact state
- gene expression shut down - histones are reorganized to help reorganize chromatin - Condensins are protein complexes (Smc4 and Smc2) which help interphase DNA produce sister chromatids of a mitotic chromosome - ATP is used as energy - about 1 condensin per 10,000 bp - SMC- Structural maintenance of chromosomes
When is gene expression shut down?
In formation of 700nm fibers
When are histones are reorganized into chromatin?
In the formation of 700nm condensed chromosomes fibers
Describe the formation of mitotic chromosomes
- Sister chromatid are held together by Cohesin protein complexes
- Cohesin: Smc1, Smc3, Scc3 and Scc1(sister chromatin cohesion complex)
- Cohesin form giant rings around the two sister chromatids during S phase and remains till the transition from metaphase to anaphase
Describe heterochromatin in detail
- interphase chromatin remains densely packed
- transcriptionally inactive
- DNA in the centromeres region and the telomeres region typically remains densely packed
- inactive satellite sequences are heterochromatic
- AT rich and is darkly stained by Geimsa