DNA and chromatin structure
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| Purines | Adenine and Guanine
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| Pyrimidine | Cytosine, Thymine (DNA) and Uracil (RNA)
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| Nucleosides | Purines or pyrimidines covalently linked to ribose or deoxyribose via N-beta-glycosidic bonds.
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| Linked to D-ribofuranose | Ribonucleosides
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| Linked to 2-deoxy-D-ribofuranose | Deoxynucleosides
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| Syn and anti comformation | Purines can exist in anti and syn conformation with anti being preferred. Pyrimidines occur in the anti conformation.
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| Nucleotides | Phosphate esters of nucleosides which can form at the hydroxyl groups at 2', 3' or 5' carbons of a ribonucleoside
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| 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
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| DNA structure | DNA is a double helix, intertwined anti-parallel. Each chain linked by phosphodiester bonds between 3'-OH and 5' phosphate group deoxyribose.
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| Chargaff's Rules | Percentage of A=T and G=C
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| 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.
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| 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.
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| DNA disruption | Heating the solution of DNA which disrupts the hydrogen bonds (reversible). They re-associate when temp is below melting(annealing).
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| Melting Temperature | Temperature at which half the helical structure is lost.
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| Other forms of separating strands | Adding acid or alkali to ionize the nucleotide bases and disrupt base pairing.
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| Hypochromism | Stacked bases in nucleic acids absorb less ultraviolet light than do unstacked bases
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| 260nm significance | Melting of nucleic acids is easily followed by monitoring their absorption of light, which peaks at wavelenght of 260nm
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| 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.
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| Genome in human dna | Each 10^14 cells approximately have their own copy of genome except RBCs which lack a nucleus.
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| Metaphase in Mitosis | Human genome can be visualized during metaphase when they are in highly condensed form.
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| Eukaryotic DNA | Packed in compact form, by being wrapped around histones to form nucleosomes.
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| Non-dividing cells (G0 and interphase) | DNA is packaged in the nuclei in complexes with various proteins and is referred to as chromatin
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| Nucleosomes make up | 50% DNA and 50% protein roughly
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| 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
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| H1 | A fifth histone binds the two DNA strands where they enter and leave the core histone which seals the assembly
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| SMC (structural maintenance of chromosomes) | SMC proteins are responsible for keeping the sister chromatids organized together during the cell cycle
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| 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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