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Structural properties of nucleotides:
Structural properties of nucleotides: Backbones are hydrophilic (pentose hydroxyls form hydrogen bonds with water), phosphates are completely ionized at pH 7.0 = negative charged, and bases "stack" to minimize contact with water.
Syn. of nucleic acid:
Nucleic acid: same thing as polynucleotide, more than 50 bases.
Polymeric form of nucleotides:
Polymeric form: 5' phosphate + 3' hydroxyl, creates backbone of pentose-phosphate-pentose-phosphate. DNA and RNA have the same backbone structure, staggered.
What are the chemical properties of nucleotides that explain DNA structures:
Chemical properties of nucleotides that explain DNA structures: (1) bases are hydrophobic (2) H-bonds form between nucleotide bases of two different strands (3) Both 1 and 2 stabilize binding between two or more strands. A + T make two hydrogen bonds and C + G make 3 hydrogen bonds.
A form of DNA:
- A Form: favored in anhydrous solutions and is a right handed helix ( favored by DNA-RNA hybrids and RNA alone).
B-Form of DNA:
B Form: Most stable in biological systems for random sequence DNA , in aqueous solution, and it is a right handed helix.
Z-form of DNA:
Z Form: Certain base sequences and high salt favor this form, it is a left handed helix, it is more elongated than A or B, it has almost no minor groove, and has a flat major groove. Short stretches found in eukaryotes and prokaryotes, plays a role in gene regulation, and it is stable. The bases are exposed and protein can bind in major groove to regulate DNA.
What are the complex polymers that result from DNA and RNA folding: what are their functions?
- Hairpins: thermodynamically favorable, it they can pair they will.
- Bulge: important kink for RNA, causes point mutation in DNA.
- Internal loop: need for RNA function, mutation in DNA.
What do specific sequences lead to structurally?
DNA sequences lead to specific DNA structures: (1) Four or more adenosine residues lead to a tight bend in the helix, causes change in direction of DNA (2) Repeated DNA sequences: (a) palindrome is the same sequence forwards and backwards (b) inverted repeats occur over 2 strands of DNA, self complimentary: hairpins and cruciforms (c) mirror repeats occur often on the same strand
describe triplex DNA:
Triplex DNA: b-form of DNA makes additional H-bonds in major groove. Special hydrogen bonds: Hoogsteen positions (the atoms that make the bonds). Non-Watson-Crick pairing: Hoogsteen paring (the bases that make the bonds). The Hoogsteen pairings add stability to DNA and the 3rd strand lays in major groove.
Tetraplex DNA: 4-stranded DNA where there is a high proportion of Guanosine residues, it is very stable. It occurs at end of chromosomes to stabilize DNA. Just think 4G.
How many H bonds to the nucleotides make?
Adenine, Thymine, and Uracil can make two H-bonds.Cytosine and Guanine can make three H-bonds.