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DNA and chromatin

DNA and chromatin structure

Purines Adenine and Guanine
Pyrimidine Cytosine, Thymine (DNA) and Uracil (RNA)
Nucleosides Purines or pyrimidines covalently linked to ribose or deoxyribose via N-beta-glycosidic bonds.
Linked to D-ribofuranose Ribonucleosides
Linked to 2-deoxy-D-ribofuranose Deoxynucleosides
Syn and anti comformation Purines can exist in anti and syn conformation with anti being preferred. Pyrimidines occur in the anti conformation.
Nucleotides Phosphate esters of nucleosides which can form at the hydroxyl groups at 2', 3' or 5' carbons of a ribonucleoside
Nucleic acids Polymers of nucleotides joined by diester bonds linking the 3'-OH in the sugar of one nucleotide with the 5'-PO4 in the sugar of the adjoining nucleotide
DNA structure DNA is a double helix, intertwined anti-parallel. Each chain linked by phosphodiester bonds between 3'-OH and 5' phosphate group deoxyribose.
Chargaff's Rules Percentage of A=T and G=C
Structural forms of DNA B-most common, right handed. A-right handed. Z-left handed. Dehydration induces transition from B to A DNA. Z can be formed in regions in which purines alternate with pyrimidines.
RNA stability vs. DNA stability The 2'hydroxyl group makes RNA susceptible to base-catalyzed hydrolysis, which results in cleavage of the phosphodiester backbone. The removal decreases the rate of hydrolysis by 100 fold.
DNA disruption Heating the solution of DNA which disrupts the hydrogen bonds (reversible). They re-associate when temp is below melting(annealing).
Melting Temperature Temperature at which half the helical structure is lost.
Other forms of separating strands Adding acid or alkali to ionize the nucleotide bases and disrupt base pairing.
Hypochromism Stacked bases in nucleic acids absorb less ultraviolet light than do unstacked bases
260nm significance Melting of nucleic acids is easily followed by monitoring their absorption of light, which peaks at wavelenght of 260nm
E. Coli genome vs. human genome E. Coli consist of single circular DNA of ca 4 million base pairs. Human consist of ca. 3.2 billion base pairs organized into 23 pairs of chromosomes in the nucleus.
Genome in human dna Each 10^14 cells approximately have their own copy of genome except RBCs which lack a nucleus.
Metaphase in Mitosis Human genome can be visualized during metaphase when they are in highly condensed form.
Eukaryotic DNA Packed in compact form, by being wrapped around histones to form nucleosomes.
Non-dividing cells (G0 and interphase) DNA is packaged in the nuclei in complexes with various proteins and is referred to as chromatin
Nucleosomes make up 50% DNA and 50% protein roughly
Four histones Small basic proteins, a 1/4 of the residues are arginine or lysine. H2A, H2B, H3 and H4. Associate with one another to form an octamer. DNA wraps around to form 2 turns about 145bp in the 2 turns
H1 A fifth histone binds the two DNA strands where they enter and leave the core histone which seals the assembly
SMC (structural maintenance of chromosomes) SMC proteins are responsible for keeping the sister chromatids organized together during the cell cycle
How are the nucleosomes arranged? In helical array to form a series of stacked layers with a diameter of about 30nm-30nm fibers. Further compacted during mitosis to form a metaphase chromosome. Folding involves attachment to a nuclear scaffold with H1, topoisomerase 2 and SMC.
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