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DNA Structure
DNA is a polymer of nucleotides which are monomers
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Deoxyribose Sugar
2
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Nitrogen Containing Base
Nucleotides can also be called deoxyribonucleoside triphosphates
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An easy way to remember which is
which is to think of a TUC biscuit; the shape
is similar to that of the pyrimidines and the
letters of TUC represent the three bases
belonging to that group, thymine, cytosine
and uracil
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The base is attached to the first carbon and
the phosphate group to the fifth
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5’ carbon is
on the ‘top’ of the molecule and the 3’
is on the bottom
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Hydrogen bonds join two nucleotides
together (A-T, C-G)
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These are formed when an
electronegative atom (such as O or N) lie close
enough to another electronegative atom
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This is how
sequence specific enzymes/proteins work – they rely on the geometry of the
atoms – if one is even slightly out sub-optimal or no binding take place
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Because of the strength of these bonds if a breakage occurs this is DNA
damage and has to be fixed by enzyme activity – usually DNA ligase
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This means that the bond
between T and A is easier to break than C and G
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Requires less energy to break
double stranded DNA, therefore it is more efficient to begin here
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Because of the complementary nature of
nucleotides, if the sequence of one strand is known then it is possible to
deduce the other
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Van der Waals forces act
between heterocyclic rings to keep the bases apart
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This
makes sense due to the complementary nature of nucleotides – i
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where
there is A there will be a T bonded to it
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The C==O group in
thymine, the N group in adenine etc
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DNA does not just come in one ‘form
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The three
different structures vary in a number
of key areas
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Z-DNA has the most
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DNA Synthesis
DNA replication begins at a point on the DNA called the origin of replication
site
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Single-stranded
binding proteins react with and stabilise this single-stranded portion of DNA
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Note that DNA polymerase can only add new DNA
nucleotides to a pre-existing chain of nucleotides
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This RNA primer is a short sequence of RNA nucleotides complementary
to a small, initial section of the DNA strand being prepared for replication
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Later, the RNA primer is
enzymatically removed and replaced with an appropriate sequence of DNA
nucleotides by the enzyme nucleotide replacement enzyme
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DNA polymerase moves along the 3’ – 5’
direction, synthesizing a new 5’ – 3’ stand
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How is the 5’ – 3’ strand copied to make a new 3’ – 5’ strand? The answer is
that the 5’ – 3’ strand is copied dis-continuously by means of Okazaki
fragments
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As these
fragments are synthesized the RNA primers are removed by the nucleotide
replacement enzyme
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This is also why PCR works
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e
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We can make artificial primers specially
designed to detect specific base sequences
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During
the PCR the primers bind to the specific sequence and polymerase synthesises
from where the primer is bound
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We can then use gel electrophoresis and
immunofluorescent blotting to see if the gene of interest is present
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What is the Difference between DNA and RNA?
 RNA contains uracil instead of thymine
 RNA is largely single stranded
o DNA is double stranded
o Single stranded RNA can fold into complex 3D shapes, some have
catalytic activity
 RNA uses the ribose sugar (hence RNA)
Note that DNA polymerase can and does make mistakes in replication
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This is
called 3’-5’ endonuclease activity
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Mice had the proofreading ‘part’ of DNA polymerase delta and epsilon knocked
out
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The results are shown in the graph below
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Within the single KO the deletion of epsilon had a much greater
reduction on the life span of the mice than the delta deletion

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