chromatin

Question 1

nucleosides (5)

Answer 1

adenosine/guanosine/cytidine/thymidine/uridine

Question 2

purine bases

Answer 2

adenine, guanine

Question 3

pyrimidine bases

Answer 3

thymine, cytosine, uracil

Question 4

Chromatin/chromosome/chomatid

Answer 4

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.

Question 5

Cell cycle steps

Answer 5

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.

Question 6

Mitosis phases

Answer 6

Interphase
Prophase
Metaphase
Anaphase
Telophase

Question 7

Compact vs. loose chromatin

Where is the compact chromatin found, in the cell and in the chromosomes?

Answer 7

Heterochromatin/euchromatin.

In the cell: near the nuclear membrane and nucleolus.
In the chromosome: 
- near the centromeres
- in the telomers
- in highly repetitive sequences

Question 8

Metaphase chromosome size

Answer 8

~30nm fiber

Question 9

Chromosome light/dark bands. Name of the bands?

Answer 9

Dark regions - heterochromatic, late-replicating, AT-rich.

Bright regions - euchromatic, , early-replicating, GC-rich.

Name: Giemsa (G)-bands.

Question 10

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?

Answer 10

• 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.

Question 11

How are nucleosomes’ positions affected?

Answer 11

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.

Question 12

What is “translational positioning”?

Answer 12

Translational positioning: localization of a DNA-binding site between nucleosomes makes it accessible while incorporation into a nucleosome makes it inaccessible

Question 13

What are accessory proteins? (4)

Answer 13

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.

Question 14

What are “hypersensitive sites”? How are they generated?

Answer 14

Less compact nucleosomal structure, DNA is more available for protein binding, TFs and DNAses.

Generated by binding of proteins that exclude histones.

Question 15

What are histone tails? How can they be affected, and by what?

Answer 15

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.

Question 16

How does DNA methylation work? What effects does it have?

Answer 16

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.

Question 17

What can DNA methyl-binding proteins do? (4)

Answer 17

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.

Question 18

What is “genomic imprinting”?

Answer 18

Silencing of genes on either the maternal or the paternal chromosome.

Question 19

What are the mechanisms for movement in the genome? (2)

Answer 19

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.

Question 20

DNA transposons, LTR elements, and non-LTR elements

Answer 20

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.