Nucleic Acid Structure

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Nucleic Acid Structure

• Structure of nucleotides
• Nitrogenous bases
• Pentose sugars
• Nucleosides
• Nucleotides
• Nucleotide chains
• Structure of B-DNA
• Images accompanying this lecture may be found
  athttp//www.prenhall.com/klug4/Select chapter
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A. Structure of Nucleotides

• A nucleotide is composed of
• A nitrogenous base
• A pentose sugar
• A phosphate group

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Nitrogenous Bases

• Two different classes of aromatic carbon-nitrogen
  heterocycles
• Purines
• Adenine (Found in DNA RNA)
• Guanine (Found in DNA RNA)
• Pyrimidines
• Cytosine (Found in DNA RNA)
• Thymine (Found in DNA)
• Uracil (Found in RNA)

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C. Pentose Sugars

• Ribose
• Found in RNA
• Forms a 5-atom ring structure in aqueous solution
• Carbons are numbered 1 (one-prime), 2, 3, 4,
  5

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C. Pentose Sugars

• Deoxyribose
• Found in DNA
• Identical to ribose, except that the -OH group
  on the 2 carbon is replaced with an -H

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D. Nucleosides

• Nucleoside
• A pentose sugar molecule with a nitrogenous base
  attached to the 1 carbon
• Nucleosides are named by using the root of the
  base name, plus the suffix -osine (for purines)
  or -idine (for pyrimidines)
• Nucleosides with deoxyribose sugars are
  designated with the prefix deoxy-

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D. Nucleosides
Ribonucleosides Deoxyribonucleosides
Adenosine Deoxyadenosine
Guanosine Deoxyguanosine
Cytidine Deoxycytidine
Uridine -
- Deoxythymidine
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E. Nucleotides

• Nucleotide
• A nucleoside with one, two, or three phosphate
  groups attached to the 5 carbon
• Nucleotides are named using the name of the
  nucleoside plus monophosphate, diphosphate,
  or triphosphate depending on the number of
  phosphates
• Nucleotides with one phosphate may also be named
  by changing the nucleoside suffix to -ylic
  acid

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E. Nucleotides
Ribonucleotides Deoxyribonucleotides
Adenosine monophosphate Deoxyadenosine monophosphate
Guanosine monophosphate Deoxyguanosine monophosphate
Cytidine monophosphate Deoxycytidine monophosphate
Uridine monophosphate -
- Deoxythymidine monophosphate
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F. Nucleotide Chains

• The 5 carbon of one nucleotide can be linked to
  the 3 carbon of another nucleotide via a
  phosphodiester bond
• An oligonucleotide chain (polynucleotide chain)
  is a linear chain of nucleotides linked in this
  fashion
• The oligonucleotide chain has two ends 5 and 3

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G. Structure of B-DNA

• In the 1940s, Chargaff discovered that the DNA
  isolated from most sources exhibited a 11 molar
  ratio of AT, and a 11 ratio of GC (as compared
  to RNA, in which the AU and GC ratios are
  random)

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G. Structure of B-DNA

• In the early 1950s, Watson, Crick, and Franklin
  studied the X-ray diffraction patterns of
  crystalline DNA fibers, and determined that DNA
  had a symmetrical 3-D structure in the form of a
  helix

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G. Structure of B-DNA

• Watson Crick knew of Chargaffs ratios, and
  realized that they could build a helical model
  for DNA structure, consistent with the X-ray data

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G. Structure of B-DNA

• The Watson and Crick model is known as a B-DNA
  helix, and it is believed to be the native
  conformation of most DNA found in living organisms

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G. Structure of B-DNA

• Features of the B-DNA helix
• Two oligonucleotide strands
• The sugar-phosphate backbones of the strands are
  on the outside, and twist around a central axis
  to form a helix
• The helical twists form two groovesthat turn
  around the axis the major groove and the minor
  groove
• Therefore, DNA is a pretty groovy molecule

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G. Structure of B-DNA

• The two strands are in antiparallel orientation
  (one strand goes from 5 ? 3 and the other
  strand goes from3 ? 5
• These are the dimensions of the helix20 Å
  diameter10 bases per turn34 Å per turn

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G. Structure of B-DNA

• The bases are located in the center of the helix,
  with the flat planes of the bases perpendicular
  to the axis of the helix
• The bases between the two strands are paired
  with an A on one strand paired with a T on
  the other strand, and G paired with C
• This property of the strands is called
  complementarity (the two strands are said to be
  complementary to each other, thank you very much)

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G. Structure of B-DNA

• The strands are held together by noncovalent
  hydrogen bonds between the complementary pairs
  of basesA T pairs have two hydrogen bondsG
  C pairs have three hydrogen bonds

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G. Structure of B-DNA

• The two strands may be separated by heating
  (melting) the DNA, or by raising the pH with
  alkaline treatment
• Two pieces of single-stranded DNA will
  spontaneously form a helix if the strands have
  enough base complementarity

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G. Structure of B-DNA

• An interactive tutorial on DNA structure can be
  found athttp//molvis.sdsc.edu/dna/index.htm