• contain negative charges that push out DNA and into a ciricle, so DNA will wrap around self
• DNA wrap around nucleosome 1 and 3/4 times
• DNA nucleosome interaction is as relaxed a DNA as you're gonna get
• nucleosomes start stackin relative to each other to form fiber bundles
• bundles loop at scaffoldin proteins to form solenoids

methylation

acetylation

phosphorylation

ubiquitinylation

siRNA complexes

1. disrupt electrostatic interactions
2. more loose interaction between phosphodiester bonds, meaniner looser nucleosomes
3. exposes regulatory elements that allows gene expression

irreversible- methylation (inherited)

reversible- acetylation, phosphorylation, ubiquination

1. acetyl-CoA transfer acetyl group to Lys via histone acetyl transferase
2. cause loss of Lys charge, so it cant hold onto DNA
3. leads to pushing nucleosomes out of way so binding site for RNA polymerase and TF's can be exposed

• heterochromatin- condensed chromatin (gene silencing)
• euchromation- loose and open chromatin (gene expression)

Enzyme responsible for phosphorylation. Proteins that are phosphorylated

• cyclins
• replication factors and transcription factors
• scaffolding proteins
• remodeling proteins
• histon H3A and H2B interacting proteins

1. ubiquitin activated by ATP
2. ubiquitin adenylated by ubiquitin activating enzyme E1
3. E1 tranfer ubiquitin to own cysteine residues
4. ubiquitin transferred to Cys residue in ubiquitin conjugating enzyme E2
5. ubiquitin protein ligase E3 tranfer ubiquitin to Lys residue on on target protein: histone
6. ubiquitin pushes apart chromatin via steric hinderance

If you get 4 ubiquitins, you degrade the histones.

There are many GC rich regions of DNA at upstream regulatory elements of many geens. This will allow for a common modification: methylation of cytosine.

• will not bind TF's, resulting in gene silencing
• will bind proteins that stabilize the storage (unexpressible) form of chromatin

1. treat isolated DNA with sodium bisulfide → spontaneous deamination of cytosine to uradine
   1. if cytosine is methylated, no rxn occurs
2. use two different probes that are two different colors
   1. one is G (binds with cytosine)
   2. one is A (binds with urasine)
3. PCR
4. send through computer to look for different genes linked to cancer
   1. if hypermethylation of certain genes (ex: tumor suppressor genes hypermethylated means poor prognosis)

Describe the structure of 5-aza-cytosine and why it is so useful in treating chemotherapy. What is the disadvantage of this process

• structure-contains a N at the 5 position in the ring where as normal cytosine has a C at the 5 position
• way it can treat cancer
  • it is incorperatred into the DNA 
  • that 5 position is normally methylated, but it can't be with an N at that position
  • acts as suicide inhibitor for methyl acetyl transferase and blocks further methylation
    • when enzyme sees 5 aza cytosine, it will just "stop" and be sitting there
  • in doing this, it will stop the silencing of genes in a random fashion
    • this means we could turn off the good and the bad (we could turn on tumor suppressor genes and oncogenes)

visualizing the chromosome abnormalities and looking for genes that correlate with various disorders

• translocation of part of chromosome 22 to chromosome 9
• cause rearrangement of BCR/ABL protein that results in leukemia

• BCR is a Ser/Thr kinase while ABL is a Tyr kinase
  • ABL is on cell membrane
  • BCR is normally outside the cell, so it wont affect cell growth
• normally, ABL responds to growth factor
• BCR replaces the regulatory elements of ABL, so the ABL protein is always on
• ATP binds to the enzymes, so you get continued phosphorylation of proteins, leading to leukemia
• you will continually get stimuation of proliferation, decreased apoptosis in lymphocytes, disturbed interaction with cell's ECM

Describe the SKY/M-FISH technique

1. tag chromosomes in metaphase with fluorescent tags unique to each chromosome pattern
2. hybridization fragments combine with combinations of fluoroform (usually in UV range to give artificial color)
3. this will allow each chromosome to be visualized in a different color so we can detect chromosomal abnormalities

Role of polymers of ubiquitin

signal proteosomes to break down histones

• translocation of 8 to 14
• on 8 is the c-myc gene and it would go right next to IgG antibody producing cells
• antibody producing genes are always activated, so there is uncontrolled growth of antibodies