Nucleic Acids

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Nucleic Acids
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Nucleic Acids

• Linear polymers of nucleotides
• DNA or RNA
• levels of structure

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Structure

• Primary (1o)- sequence of nucleotides
• Secondary (2o)- local 3-D shape
• a-helix for DNA
• Tertiary (3o)- global 3-D shape

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Bases

• Purine- (2)
• Pyrimidine- (3)

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Pyrimidines
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Pyrimidines
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Pyrimidines
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Purines
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Physical Properties of the Bases

• planar or nearly so
• conjugated
• water insoluble
• acid and base stable
• keto-enol tautomers (dont worry about)

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Nucleosides

• Base sugar
• ß-D-ribose for RNA
• ß-D-2-deoxyribose for DNA

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Purine Nucleosides
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Nucleotides

• Base sugar phosphate
• ß-D-ribose for RNA
• ß-D-2-deoxyribose for DNA
• monophosphate, diphosphate or triphosphate

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Adenylate
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Nucleotides are Joined Together by Phosphodiester
Linkages
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DNA Structure

• DNA is a double-stranded, antiparallel a-helical
  structure held together by base pairing
• Base-pairing
• AT, GC

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B DNA

• Locations of components
• dimensions

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DNA is a Huge Molecule
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Packing Into Nucleosomes
2 each H2a H2b H3 H4 no H1 1.75 turns
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Beads on a String
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Further Packing - the Solenoid
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Further Packing - the Loop
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Further Packing - the Miniband
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Furthest Packing - the Chromosome
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Packing of a Circular Prokaryotic Chromosome
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Other Forms of DNA Exist

• B DNA predominates
• Z DNA- important in regulation
• A DNA- ?75 humidity
• C, D, E DNA - vary salt and/or humidity

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Physical and Chemical Properties of DNA

• Stacked helix because bases planar
• Acidic because of phosphodiester linkage
• decreased UV absorption due to bp
• Tm - Fig 7.25
• dilute acid and base stable

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RNA Structure

• 3 major types mRNA, tRNA, rRNA
• Base-pairing can occur

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RNA Structure
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tRNA Structure

• Cloverleaf

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tRNA Structure
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tRNA Structure

• Cloverleaf
• 75 nt
• modified bases
• adapter for protein synthesis - reads template
  AND carry amino acids

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mRNA Structure

• Linear
• variable size
• 7-methylguanine cap
• poly A tail
• template for protein synthesis

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rRNA Structure

• large size
• associated with protein
• condense a.a.

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Physical and Chemical Properties of RNA

• Acidic because of phosphodiester linkage
• variable amounts of base pairing
• dilute acid stable, but base labile

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DNA Sequencing

• Bypass content
• Sanger dideoxy
• restriction enzyme- Site-specific endonucleases
• Often palindromic
• Cleave both strands
• Many generate sticky ends

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Sticky Ends - Fig 7.28