chromatin Flashcards
(20 cards)
nucleosides (5)
adenosine/guanosine/cytidine/thymidine/uridine
purine bases
adenine, guanine
pyrimidine bases
thymine, cytosine, uracil
Chromatin/chromosome/chomatid
Chromatin: the “normal, loose state” of DNA, RNA, and Protein (nucleosomes) in the nucleus in the cells.
Chromosome: condensed form of chromatin (during mitosis).
Chromatid: the two “sister chromosomes” - the two copies.
Cell cycle steps
G0: cell cycle arrest.
G1: cell growth.
S: new DNA.
G2: error checkpoint, chromosome condensation.
M: cell division.
Cytokinesis: finishes division into two daughter cells.
Mitosis phases
Interphase Prophase Metaphase Anaphase Telophase
Compact vs. loose chromatin
Where is the compact chromatin found, in the cell and in the chromosomes?
Heterochromatin/euchromatin.
In the cell: near the nuclear membrane and nucleolus. In the chromosome: - near the centromeres - in the telomers - in highly repetitive sequences
Metaphase chromosome size
~30nm fiber
Chromosome light/dark bands. Name of the bands?
Dark regions - heterochromatic, late-replicating, AT-rich.
Bright regions - euchromatic, , early-replicating, GC-rich.
Name: Giemsa (G)-bands.
Nucleosome:
- How much DNA is wrapped around (bp)? How many turns?
- What is the nucleosome made of? How is it assembled?
- What is the linker DNA? What does it bind?
- What are the less compact and more compact models?
- 146bp, 1.76 turns.
- Two copies of H2A, H2B, H3 and H4.
H3(2) and H4(2) assemble and bind DNA.
H2A and H2B form heterodimers, then a heterotetramer, and bind DNA after H3 and H4 have bound.
DNA is wrapped around from the left. - The DNA between the histones. Binds H1.
- Less compact: 10nm fiber, “beads on a string”. No H1.
More compact: 30nm fiber, coiled helix. Has H1.
How are nucleosomes’ positions affected?
Sharp bends: pyrimidine–purine base steps (thymine/adenine (TA) or cytosine/guanine (CG)). More bendable than other steps.
Smooth bends: more bendable AT-rich sequences, altered by stiffer CG’s.
What is “translational positioning”?
Translational positioning: localization of a DNA-binding site between nucleosomes makes it accessible while incorporation into a nucleosome makes it inaccessible
What are accessory proteins? (4)
CAF-1, ASF1 = histone chaperones, deposit H3-H4-tetrameres.
Spt6 = reassembles the H3-H4 tetramere.
FACT = dissociates H2A-H2B dimers and “re-sets” them behind the position.
What are “hypersensitive sites”? How are they generated?
Less compact nucleosomal structure, DNA is more available for protein binding, TFs and DNAses.
Generated by binding of proteins that exclude histones.
What are histone tails? How can they be affected, and by what?
N- or C-terminals of the histones extending out from the core.
Can interact with other nucleosomes, recruit proteins.
Can be epigenetically modified - ex. by histone acyltransferases (HATS).
Acetylation, methylation, phosphorylation, ubiquitination.
How does DNA methylation work? What effects does it have?
Methyl groups are added onto cytosines by methyl transferases.
Methylated C’s are less chemically stable and can be deaminated, giving TpG, which might not be repaired.
Non-methylated C’s can be deaminated into UpG, which is recognized as faulty and repaired.
Methylation usually leads to suppression.
What can DNA methyl-binding proteins do? (4)
A) Remove acetyl groups = initiate silencing
B) Methylate the histones
C) Reposition the nucleosomes.
D) Methylate the histone tails –> recruit DNA methyl transferase –> methylate DNA.
What is “genomic imprinting”?
Silencing of genes on either the maternal or the paternal chromosome.
What are the mechanisms for movement in the genome? (2)
Class I: REPLICATIVE TRANSPOSITION = RNA is transcribed, copy is made and inserted somewhere else in the genome.
Class II: CUT AND PASTE = transposase binds inverted repeats around the gene, region is removed and reinserted somewhere else in the genome.
DNA transposons, LTR elements, and non-LTR elements
DNA-transposons: bounded by terminal inverted repeats (TIRs), which are transposase binding sites. Cut out of the genome, and pasted in another place.
LTR elements: virus-like, have LTRs at each end of the gene. Needed for reverse transcriptase to convert RNA to DNA.
Non-LRT elements: don’t use LTRs, but long interspersed elements (LINEs) which encode for proteins to mediate their own transposition - ex. reverse transcriptase.
