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Chapter 8 - Nucleotides and Nucleic Acids - Notes For Students
Chapter 8 - Nucleotides and Nucleic Acids - Notes For Students
both RNA and DNA are made up of nucleotides, which have three components:
1. a pentose (ribose or deoxyribose)
2. a phosphate
3. a nitrogenous base: either a purine or a pyrimidine (bound with a N--glycosyl bond to the
1 position of the pentose)
purine bases:
a fused double heterocyclic aromatic ring structure
major types in both DNA and RNA: adenine (A) and guanine (G)
pyrimidine bases:
a 6-membered heterocyclic aromatic ring
cytosine (C): found in both DNA and RNA
thymine (T): found in DNA and uracil (U): found in RNA
SEE FIGURE 8-4 (STRUCTURES OF THE MAJOR BASES you are expected to know these for the exam,
and how they link together in a chain)
formation of DNA and RNA chains joined via phosphates, where the 5-phosphate group of one
nucleotide is covalently linked to the 3-hydroxyl group of another nucleotide (phosphodiester
linkage)
backbones: alternate between pentose and phosphate groups, and the side groups are
the nitrogenous bases
DNA or RNA sequence: read from the 5 to the 3 end (the 5 end has no nucleotide at 5
position, and the 3 end has no nucleotide at 3 position)
DNA:
5' End
O
O
T
O-
P
O-
5'
O
H
3'
O
P
O-
O5'
3'
O
H
3' End
properties:
backbones of DNA and RNA chains are hydrophilic
OH groups on the sugars H-bond with water
phosphates (pKa ~0): negatively charged at pH 7 (charges are neutralized by ionic
interactions with proteins, metal ions, etc)
pyrimidines and purines:
weakly basic
hydrophobic and mostly insoluble in water at neutral pH (under acidic or basic
conditions the bases become charged and a little more water-soluble)
engage in hydrophobic stacking interactions (planes of the rings are parallel),
mediated in part by van der Waals interactions. Stacking minimizes contact
between the bases and water (and stabilizes the double helix structure)
H-bonding between bases (i.e. base-pairing) allows for complementary association
between two strands of DNA or RNA.
most important base pairs: A=T and GC. There is a stronger interaction
between G and C due to three hydrogen bonds, compared to two between A
and T (or A and U). SEE FIGURE 8-11.
DNA can also adopt unusual structures in regions of the sequence that are palindromes (inverted
repeats with symmetry over two strands):
since these regions are self-complementary, hairpin or cruciform structures can form SEE
FIGURES 8-18 and 8-19
RNA structure:
can form anti-parallel double helix with another RNA strand or with DNA.
single-stranded RNA can also form very complex structures with hairpin structures and
pairing of self-complementary sequences SEE FIGURE 8-24