Chemistry 501 Handout 8 Nucleotides and Nucleic Acids Chapter 8

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Chemistry 501 Handout 8 Nucleotides and
Nucleic AcidsChapter 8
Lehninger. Principles of Biochemistry. by Nelson
and Cox, 5th Edition W.H. Freeman and Company
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Structure of nucleotides
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Major purine and pyrimidine bases of nucleic
acids
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Conformation of ribose
same side of the plane relative to the C-5 atom
opposite side of the plane relative to the C-5
atom
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Ribonucleotides of nucleic acids
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Deoxyribonucleotides of nucleic acids
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Some minor purine and pyrimidine bases, shown as
the nucleosides
Minor bases of DNA
Minor bases of tRNAs
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Some adenosine monophosphates
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Hydrolysis of RNA under alkaline conditions
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Phosphodiester bonds link successive nucleotides
in nucleic acids
Phosphodiester linkages in the covalent backbone
of DNA and RNA
Some adenosine monophosphates
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Schematic representation of the nucleotide
sequences of nucleic acids
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The properties of nucleotide bases affect the
three-dimensional structure of nucleic acids
Free pyrimidine and purine bases may exist in two
or more tautomeric forms depending on the pH.
As a result of resonance, all nucleotide bases
absorb UV light.
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Hydrogen-bonding patters in the base pairs
defined by Watson and Crick
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Watson-Crick model for the structure of DNA
X-ray diffraction pattern of DNA
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Complementarity of strands in the DNA double
helix
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Replication of DNA as suggested by Watson and
Crick
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DNA can occur in different three-dimensional forms
Structural variations in DNA
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Comparison of A, B, and Z forms of DNA
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Certain DNA sequences adopt unusual structures
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DNA structures containing three or four DNA
strands
Hoogsteen pairing
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Messenger RNAs code for polypeptide chains
Messenger RNA is only one of several classes of
cellular RNA
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The product of transcription of DNA is always
single-stranded RNA. The single strand tends to
assume a right-handed helical conformation
dominated by base-stacking interactions.
Bases P atoms Riboses and phosphate oxygens
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Secondary structure of RNAs
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Base-paired helical structures in an RNA
Non Watson-Crick base pairs
Complementary sequences that may be paired in the
3D structure
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Three-dimensional structure in RNA
Some unusual base-pairing patters found in this
tRNA
Phenylalanine tRNA of yeast
A hammerhead ribozyme from a plant virus
An intron (segment of mRNA) from the ciliated
protozoan Tetrahymena thermophila
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Double-helical DNA and RNA can be denatured
Reversible denaturation and annealing
(renaturation) of DNA
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Heat denaturation of DNA
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Partially denatured DNA
Bubbles Regions rich in AT base pairs
specifically denature, while most DNA remains
double-stranded
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Nucleic acids from different species can form
hybrids
DNA hybridization
Can be used to detect similar DNA sequences in
two different species or within the genome of a
single species
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Nucleotides and nucleic acids undergo
nonenzymatic transformations
In DNA, uracil residues are removed by the
repair system
100 per day per cell
10,000 per day per cell
1 per day per cell
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Formation of pyrimidine dimers induced by UV
light
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Alkylating agents can alter certain bases of DNA
Cannot base-pair with cytosine
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Chemical agents that cause DNA damage
Deaminating agents
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The sequences of long DNA strands can be
determined
DNA sequencing by the Sanger method
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Strategy for automating DNA sequencing reactions
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dimethoxytrityl
The chemical synthesis of DNA has been automated
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Nucleotides carry chemical energy in
cells. Adenine nucleotides are components of
many enzyme cofactors. Some nucleotides are
regulatory molecules.
Other functions of nucleotides
Nucleoside phosphates
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The phosphate ester and phosphoanhydride bonds of
ATP
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Some coenzymes containing adenosine
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Three regulatory nucleotides