MHG 2: Structure of DNA II

Question 1

What are the benefits of underwinding in DNA?

Answer 1

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.

Question 2

histone H1

Answer 2

–vital for compacting DNA from 10nm fibers to 30nm fibers –located at the DNA entry/exit point on the nucleosome

Question 3

nucleosome formation

Answer 3

–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)

Question 4

histone fold

Answer 4

3 alpha helices held together by 2 short strands of DNA, forms nucleosome core

Question 5

salt bridges

Answer 5

formed between positive charges (arginine and lysine) on histone and negative charges from phosphate backbone on DNA

Question 6

H3 tail

Answer 6

acts like a receptor and becomes phosphorylated or acetylated to turn on/off gene expression

Question 7

hexagonal structure

Answer 7

six H1 domains can link their nucleosomes together repeats of hexagonal structures form 30nm fibers

Question 8

30 nm loops

Answer 8

predominate form of DNA, attach to nuclear scaffold or inner nuclear membrane by nuclear lamins, 100X compaction of DNA

Question 9

looped domains

Answer 9

1,000X compaction

Question 10

mitotic chromosomes

Answer 10

10,000 to 100,000 X compaction

Question 11

DNA methylation and de-acetylation

Answer 11

inactivates DNA and condenses DNA

Question 12

DNA de-methylation and acetylation

Answer 12

activates DNA and unwinds DNA

Question 13

P90rsk2

Answer 13

phosphorylates serine 10 on the H3 tail; generally activating for both unwinding and condensation

Question 14

Transcriptional Activation: histone acetyltransferases (HATs)

Answer 14

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

Question 15

condensins

Answer 15

allow for greater condensation primarily during the M phase of the cell cycle

Question 16

cohesions

Answer 16

during the S phase of the cell cycle cohesions are added to the DNA for greater compaction

Question 17

steps for DNA compaction

Answer 17

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

Question 18

steps for DNA activation

Answer 18

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**

Question 19

ICF syndrome

Answer 19

autosomal recessive mutation, rare, caused by mutation in DNMTB3 gene, causes hypomethylation

Question 20

symptoms of ICF syndrome

Answer 20

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

Question 21

Rett syndrome

Answer 21

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

Question 22

Coffin-Lowry syndrome

Answer 22

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

Question 23

Rubenstein-Tayibi syndrome

Answer 23

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

Question 24

transposons

Answer 24

about 50% of human genome consists of transposons

Question 25

short sequence repeats (AKA satellite DNA)

Answer 25

found in centromeres and telomeres, less than 10 bp long, 3% of genome, do not code for protein but provide structure,

Question 26

satellite 2

Answer 26

pericentric on chromosomes 1, 9, and 16, methylation occurs here so the spindle apparatus during mitosis can attach

Question 27

pericentric

Answer 27

related to the centromere of the chromosome

Question 28

telomeres and simple sequence repeats

Answer 28

TTAGGG, a few telomeric repeats are lost every cell division, eventually vital genes are exposed and the cell dies

Question 29

of genes in the genome

Answer 29

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

Question 30

structure of a nucleosome

Answer 30

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%

Question 31

size of a nucleosome

Answer 31

11 nm diameter X 6 nm thickness

Question 32

topoisomerases

Answer 32

create negative supercoil for DNA to wrap around histone core

Question 33

Rett syndrome symptoms

Answer 33

Deceleration in head growth, loss of speech and hand use, repetitive hand movements. Sometimes autism, apraxia, breathing dysfunction