Chapter 8.2: Structure

• The primary structure of nucleic acids is the covalent structure and nucleotide sequence.
• The secondary structure of nucleic acids is the regular stable structure taken up by some or all the nucleotides.
• The tertiary structure of nucleic acids is the complex folding of large chromosomes or the elaborate folding of tRNA and rRNA structures.
• X ray diffraction patterns revealed DNA molecules are helical.
• Offset pairing of the two strands creates a major and minor groove.
• Major grooves expose more the nucleotides the to environment.
• Minor grooves expose less of the nucleotides to the environment.
• There are three hydrogen bonds between G and C.
• There are two hydrogen bonds between A and T.
• Parallel arrangement is when 3', 5' phosphodiester bonds run in the same direction.
• Antiparrallel arrangement is when 3', 5' phosphodiester bonds run in the opposite direction.
• The antiparrallel arrangement of DNA was confirmed by x ray analysis.
• The offset pairing of the two strands creates a major groove and a minor groove on the surface of the duplex.
• The double helix has 10.5 base pairs per helical turn and is about 36 A long.
• Double helix DNA strands are complementary.
• When adenine occurs on one chain, thymine is found in the other.
• When guanine occurs in one chain, cytosine is found in the other.
• Hydrogen bonding does not contribute significantly to stability of the structure.
• The double helix is stabilized by the metal cations that shield the negative charges of the backbone phosphates and the base stacking interactions between successive base pairs.
• Successive guanine cytosine hydrogen bonds are stronger than successive adenine thymine hydrogen bonds.
• Duplexes with a higher guanine cytosine content are more stable.
• Pyrimidines and purines are aromatic
• Step one of DNA replication is the preexisting parent strands become separated.
• Step two of DNA replication is each parent strand serves as a template for the biosynthesis of a complementary daughter strand.
• Structural variation in DNA reflects different possible conformations of deoxyribose, rotation about the contiguous bonds making up the phosphodeoxyribose backbone, and free rotation about the C1'-N-glycosyl bond.
• The B form of DNA is the Watson Crick structure.
• The B form of DNA is the most stable for a random sequence DNA molecule under physiological conditions.
• The A form of DNA is a right handed double helix with a wider helix, 11 base pairs per turn, and a tilted plane.
• The A form is favored in situations devoid of water.
• The Z form of DNA is a left handed helix with 12 base pairs per turn and a backbone with a zig zag appearance.
• The Z form of DNA appears more slender and elongated.
• Diagram

  A) A form

  B) B form

  C) Z form

  D) B form

  E) A form

  F) Z form

  G) A form

  H) B form

  I) Z form

  
• The helical sense in A form is right handed, B form is right handed, and Z form is left handed.
• The diameter of A form is 26A, B form is 20A, and Z form is 18A.
• The base pairs per turn in A form is 11, B form is 10.5, and Z form is 12.
• The helix rise per base pair in A form is 2.6A, B form is 3.4A, and Z form is 3.7A.
• The base tilt normal to the helix axis in A form is 20, B form is 6 and Z form is 7.
• The sugar pucker conformation in A form is C-3' endo, B form is C-2' endo, and Z form is C-2' endo for pyrimidines and C-3' endo for purines.
• The glycosyl bond conformation in A form is anti, B form is anti, and Z form is anti for pyrimidines and syn for purines.
• A palindrome is a region of the DNA that is identical when read either forward or backward. This is applied to regions of DNA with inverted repeats.