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DNA and Replication
Fig. 5-27
Making a
nucleotide
5 end
5C
Nitrogenous bases
Pyrimidines
3C
Nucleoside
Nitrogenous
base
Cytosine (C)
Thymine (T, in DNA) Uracil (U, in RNA)
Purines
Phosphate
group
5C
Sugar
(pentose)
Adenine (A)
Guanine (G)
(b) Nucleotide
3C
Sugars
3 end
(a) Polynucleotide, or nucleic acid
Nitrogenous base connected to 1’ carbon
of sugar – nucleoside
Phosphate group added to 5’ carbon of
sugar - nucleotide
Deoxyribose (in DNA)
(c) Nucleoside components
Ribose (in RNA)
DNA is a linear polymer of nucleotide
subunits joined together by phosphodiester
bonds - covalent bonds between phosphate
group at 5’ carbon and 3’ carbon of next
nucleotide – uses oxygens as bridges.
5’ C
(free)
Chain of nucleotides has alternating sugar
and phosphate components, called the “sugarphosphate backbone.” Nitrogenous bases stick
off backbone at regular intervals.
Note that any linear chain of nucleotides has
a free 5’ C on one end, and a free 3’ C on
the other. A chain of DNA thus has
POLARITY! The polarity of this strand is
5’ -> 3’, top to bottom.
3’ C
5’ C
1’ C
3’ C
(free)
Fig. 16.5
All strands of DNA look like this, there is no
variability in the sugar phosphate backbone.
They differ in the identities of the
nitrogenous bases at any given position – they
have different DNA sequences. A simple way
to represent this strand of DNA is:
5’-TACG-3’
Segments of this sequence, which can be
100s to 1000s of nucleotides long, are the
genes that code for single, specific proteins.
5’ C
(free)
RNA
Sugar is ribose
Nitrogenous bases are A G C U
This is form of most RNAs in our
cells.
DNA
Sugar is deoxyribose
Nitrogenous bases are A G C T
DNA takes structure one step
further – almost always exists as
a double helix.
free 3’ C
Fig. 16.5
Fig. 16.7
major
groove
minor
groove
In a double helix, 2 strands of DNA wrapped around each other in shape of helix
Strands are held together by hydrogen bonding between nitrogenous bases. Weak
interactions, but strength in numbers
Only pairings that work are A with T and G with C. Strands held at constant
distance from one another because of the similar geometry of A-T and G-C base
pairs
Also, only way pairings will work is if strands have opposite polarity
The only pairings that work are A-T (2
H-bonds) and G-C (3 H-bonds). These
are called nitrogenous base pairs (or
simply base pairs).
Note that A-T and G-C base pairs both
contain a purine and a pyrimidine – similar
geometry, same overall diameter.
Fig. 16.8
5’
3’
The two strands of the DNA double
helix are COMPLEMENTARY to each
other. Means that when oriented with
opposite polarity, their nitrogenous
bases are in sequence to form perfect
Watson-Crick base pairs.
5’
3’
3’
5’
3’
5’
Watson and Crick suggested
that to replicate DNA, strands
were separated by breaking
weak hydrogen bonds between
base pairs. Each strand then
has information to direct
synthesis of new complementary
strand to form 2 double helices.
DNA POLYMERASE
(in E. coli, three versions, I, II, and III)
Uses triphosphate forms
of nucleotides as
precursors.
Cannot initiate new
strand, can only ADD
nucleotides to 3’ end of
growing strand that are
complementary to
template strand.
Synthesis ALWAYS in 5’
to 3’ direction.