BC 13 Chromatin Flashcards
Nucleoside
Nucleotide
Nucleoside: Base linked to a sugar (without phosphates)
Nucleotide: nitrogenous base linked to a sugar (ribose or deoxyribose) and 1 to 3 phosphates (mono di tri)
Draw nucleotide triphosphates and deoxynucleotide triphosphates
positions of molecules on sugar ring
1' C- base 2' C- OH (ribose) H (deoxyribose) 3' C- OH 4' C - branch 5' C- off ring, phosphoester bond
linkage of DNA molecules
Phosphodiester bonds between sugars linking the 3’ OH with phosphate of the 5’ C of thenext nucleotide
DRAW
Ends
5’ linked to phosphate, and 3’ to an O
-3’ C is the site of New nucleotide incorporation
ALWAYS BUILT IN 5’ -> 3’ orientation
Purines
Adenine and Guanine
TWO RING structure
pyrimidines
Cytosine and Thymine and Uracil
ONE RING structure
base pairs
G-C - three H bonds
A-T - two H bonds
A-U RNA only two H Bonds
Stabilize dsDNA, more H bonds
Transcription Check #1
correct H bonding between single stranded DNA and unincorporated ribonucleotides facilitates the addition without error
DNA replication Check #1
primarily determined by H bonding. Damage to a nucleotide that changes its H bonding characteristics will result in the twong nucleotide being incorporated
dsDNA
Right handed helix
stacked parallel in dinner plate fashion
no bulging, same length bond between all bonds
negative phosphodiesters on periphery of helix
Surface Grooves:
- Major: wide and deep
- minor: narrow and deep
- DNA binding protiens distinguish between grooves by recongnizing different patters of potential H bond donors and acceptors.
dsDNA stabilization
hydrogen bonding
base stacking (Van Der Waals) -between bases on the same strand
Ionic Bonding: between negatively charged phosphate backbone and positively charged cations. Shields negative charge repulsion between groups.
Melting Point
Tm generally 95, higher with high GC content
Histones
Organize DNA, 10nm wide, beads on a string
nucleosome: DNA and histone complex every 20-80bp connected by linker DNA
H1 outside nucleosome: other 4 are inside (x2)
FURTHER CONDENSED 30nm fiber
Nucleosome
146 bp wraps 1.75 times 8 core histones
chromatosome includes H1(ninth) and is 165 bp
DNA coiling
naked DNA (transcriptionally active)
10nm Fiber beads
30nm Fiber of packed nucleosomes
LOOP domains
Condensed section
Fully condensed and transcriptionally inert
linker DNA
non nucleosome regions of DNA often associated with transcription factors bound to promoters
histone tails
stretches of amino acids at the N terminous of each histone protein that protrude from the nucleosome
more susceptible to enzymes and post trans modifications like acetylation
histone acetylation (lysine)
pos charged lysine residues within histone tails interact with negatively charged backbone of DNA holding it in place
acetylation of lysine residues removes the positive charge, and destabilizes this interaction.
DNA around nucleosome begins to loosen
HAT: histone acetyltransferase: LOOSEN
HDAC: histone deacetylases: remove and TIGHTEN
additional histone modifications
lysine residues can also undergo methylation
serine and threonine residues can undergo phosphorylation.
these modifications TYPICALLY
Constitutive Heterochromatin
Facultative Heterochromatin
CH: DNA sequences that are generally not transcribed (centromeres, telomeres)
FH: contains genes that are not transcribed in that particular cell but may be transcribed in others
