Nucleotides and nucleic acids

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Nucleotides and nucleic acids

• Lecture 5
• Dr. Mamoun Ahram

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Nucleic acids

• Monomers
• Polymers

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Chemical composition and bonds
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DNA vs. RNA
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Nitrogenous bases
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Other nucleotides

• Xanthine, hypoxanthine and uric acid
• intermediates in purine metabolism)
• N6-methyl adenine
• 5-methyl-cytosine and N4-methyl cytosine
• pseudouracil
• has the ribose attached to C5 instead of N1 of
  uracil
• Pseudouridine
• 1,3,7-trimethylxanthine (caffeine)

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Nucleotides are acidic
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Nucleotides vs. Nucleosides
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Nucleic acid polymer
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A new era
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DNA structure

• A double helix
• Backbone vs. side chains
• Antiparallel
• Specific base-pairing
• Chargaff's rules
• Stable
• Flexible
• Groovings
• Stability vs. flexibility
• Chargaff's rules

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Chemical forces

• Ionic interactions
• Hydrogen bonds
• van der Waals interactions
• Hydrophobic interactions (Base stacking)
• Both van der Waals and hydrophobic interactions
  drive the formation of DNA (and RNA) double
  helices

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B-DNA
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Other forms
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Chromosomal packaging

• 2 meters of DNA/cell
• 40 km of thread in a tennis ball!
• How?
• Histones

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What is a chromatin?

• Chromatin DNA molecule proteins
• The proteins that bind to the DNA
• histones (H1, H2A, H2B, H3, and H4)
• nonhistone chromosomal proteins

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Nucleosomes
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Chromatosome

• H1 is bound to the DNA forming with the octamer
  and wrapped DNA a chromatosome

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DNA-histone interaction

• Histones are positively charged
• Interaction
• Charge neutralization

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RNA

• Vs. DNA
• Secondary structures

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Molecular processes
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Types of RNAMessenger RNA (mRNA)

• Localization
• Modification
• Variable size

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Types of RNARibosomal RNA (rRNA)

• Ribosomal RNA molecules comprise 65 to 70 of the
  mass of the ribosome
• The rRNA maintains the structure of the ribosome
  and provides sites for the binding of mRNA and
  protein synthesis

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Types of RNATransfer RNA (tRNA)

• tRNA is a 75 base molecule that carries the
  amino acids, and transfers them to the growing
  protein
• tRNAs have a common tertiary structure

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Modified nucleotides in tRNA

• tRNAs contain modified bases

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Other RNA molecules

• Small nuclear RNA (snRNA)
• RNA processing
• MicroRNA (miRNA)
• Natural
• translation regulation
• Small interfering RNA (siRNA)
• Synthetic
• Translation regulation

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Light absorbance of nucleic acids

• Aromatic pyrimidines and purines can absorb UV
  light
• The peak absorbance is at 260 nm wavelength

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The unit of absorbance

• The absorbance of 260 nm (A260) is constant
• dsDNA A260 of 1.0 50 ug/ml
• ssDNA of 1.0 30 ug/ml
• ssRNA A260 of 1.0 40 ug/ml

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Exercise

• What is the concentration of a double stranded
  DNA sample diluted at 110 and the A260 is 0.1?
• DNA concentration 0.1 x 10 x 50 µg/ml
• 50 µg /ml

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Denaturation-renaturation
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Observation of denaturation
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Factors influencing Tm

• GC pairs
• pH
• Salt and ion concentration
• Destabilizing agents (alkaline solutions,
  formamide, urea)

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G-C content