MHG 2: Structure of DNA II Flashcards
What are the benefits of underwinding in DNA?
1.) compaction of the DNA because underwinding allows it to wrap around nucleosome 2.) storage of potential energy to facilitate opening 3.) potential to twist in the opposite direction and make Z-DNA 4.) ability to form hairpins and cruciform loops.
histone H1
–vital for compacting DNA from 10nm fibers to 30nm fibers –located at the DNA entry/exit point on the nucleosome
nucleosome formation
–H2A and H2B associated together (as heterodimer), H3 and H4 associate together (as heterotetramer) –C terminals facing outward (hydrophilic), N terminals buried in the histone core (hydrophobic)
histone fold
3 alpha helices held together by 2 short strands of DNA, forms nucleosome core
salt bridges
formed between positive charges (arginine and lysine) on histone and negative charges from phosphate backbone on DNA
H3 tail
acts like a receptor and becomes phosphorylated or acetylated to turn on/off gene expression
hexagonal structure
six H1 domains can link their nucleosomes together repeats of hexagonal structures form 30nm fibers
30 nm loops
predominate form of DNA, attach to nuclear scaffold or inner nuclear membrane by nuclear lamins, 100X compaction of DNA
looped domains
1,000X compaction
mitotic chromosomes
10,000 to 100,000 X compaction
DNA methylation and de-acetylation
inactivates DNA and condenses DNA
DNA de-methylation and acetylation
activates DNA and unwinds DNA
P90rsk2
phosphorylates serine 10 on the H3 tail; generally activating for both unwinding and condensation
Transcriptional Activation: histone acetyltransferases (HATs)
occurs during INTERPHASE when gene is supposed to be ACTIVE, acetylate lysines 9 and 14 of the H3 tail to initiate the unwinding of the DNA from the histone core
condensins
allow for greater condensation primarily during the M phase of the cell cycle
cohesions
during the S phase of the cell cycle cohesions are added to the DNA for greater compaction
steps for DNA compaction
1.) DNMT3B does de novo methylation of GC islands on one strand, DNMT1 does maintenance methylation on the complementary strand GC island (usually in the promoter region) 2.) Methylation attracts MeCp2 to this region. 3.) MeCP2 attracts class I histone deacetylases (HDACs 1, 2 and 8) to remove the H3 acetylations 4.) MeCP2 attracts the H1 histone necessary for compaction 5.) Phosphorylation of the H3 tail occurs at serine 28
steps for DNA activation
1.) P90rsk2 phosphorylates serine 10 2.) HATs acetylate lysines 9 and 14 on the H3 histone tail 3.) The acetylated tail attracts CREB-binding protein (CBP), which is another HAT that further acetylates the nucleosome and causes H1 to dissociate. **Acetylation decreases the overall positive charge of the histones to disrupt the salt bridges with DNA**
ICF syndrome
autosomal recessive mutation, rare, caused by mutation in DNMTB3 gene, causes hypomethylation
symptoms of ICF syndrome
1.) immunodeficiency–fragmented white bloods cells, 2.) Centromeric instability-particularly of satellite 2 DNA, karyotyyping can help confirm this disease 3.) Facial anomalies result from misexpression of vital genes for cranio-facial and cerebral development
Rett syndrome
X-linked dominant disorder, 1 in 10,000 girls because the boys usually die, MeCP2 mutation results in inability to condense chromatin, confirmed with a blood test usually during infancy, restoring levels of MeCP2 protein can relieve the symptoms, neurologic symptoms, NT malfunctions
Coffin-Lowry syndrome
disorder of chromatin activation, X-linked dominant, mutations in RSK2 protein, which no longer phosphorylates serine 10 on the H3 tail or recruits HATs; results in hypoacetylation, RSK 2 also has an active role in cell signaling; facial dysmorphism, skeletal deformation, abnormal digits
Rubenstein-Tayibi syndrome
affects 1 in 125,000 people, autosomal dominant; due to a insufficiency of CBP function–>hypoacetylation; also a coactivator for some bone morphogenic proteins (BMPs), this syndrome will lead to skeletal abnormalities and mental retardation
transposons
about 50% of human genome consists of transposons
short sequence repeats (AKA satellite DNA)
found in centromeres and telomeres, less than 10 bp long, 3% of genome, do not code for protein but provide structure,
satellite 2
pericentric on chromosomes 1, 9, and 16, methylation occurs here so the spindle apparatus during mitosis can attach
pericentric
related to the centromere of the chromosome
telomeres and simple sequence repeats
TTAGGG, a few telomeric repeats are lost every cell division, eventually vital genes are exposed and the cell dies
of genes in the genome
30% code for genes, 1% code for exons, rest of the 30% codes for promoters, introns and regulatory sequences, 20-25K genes in the human genome
structure of a nucleosome
8 histone subunits, 146 bps of DNA wrapped 1.65 times around the histone core, 56 bp linker region, DNA typically underwound by 1 turn/nucleosome, 10 nm fiber underwound by 5-7%
size of a nucleosome
11 nm diameter X 6 nm thickness
topoisomerases
create negative supercoil for DNA to wrap around histone core
Rett syndrome symptoms
Deceleration in head growth, loss of speech and hand use, repetitive hand movements. Sometimes autism, apraxia, breathing dysfunction
