Chapter 8.2: Structure

Cards (69)

  • 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.