DNA structure and
replication
BioCoach Module
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This BioCoach module is designed to help you understand DNA structure and replication.
As you solve problems, you will be reviewing the chemical structure of DNA and the
process of DNA replication. Animations and interactive activities will enrich your review
experience in a dynamic way. This module is designed to be a supplement to, but not a
replacement for, your textbook and classroom notes.
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Concept 1: The Nucleotide
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The basic building block of DNA is the
nucleotide.
The nucleotide in DNA consists of a sugar (deoxyribose), one of four bases (cytosine (C),
thymine (T), adenine (A), guanine (G)), and a phosphate. Cytosine and thymine are
pyrimidine bases, while adenine and guanine are purine bases. The sugar and the base
together are called a nucleoside.
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The basic building block of DNA is the
nucleotide.
The three parts of the nucleotide building block of DNA are the
sugar, the base and the phosphate. The complex of the sugar
with the base is called a nucleoside.
The sugar is the 5-carbon sugar deoxyribose. By convention the carbons on this sugar are
labeled 1' through 5’.
The phosphate is attached to the 5' carbon of the deoxyribose sugar.
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The basic building block of DNA is the
nucleotide.
The base is attached to the 1' carbon of the deoxyribose sugar. There are four different
bases found in DNA. Because each base contains at least two nitrogen atoms, they are
called nitrogenous bases. There are two classes of bases, the pyrimidines (cytosine (C)
and thymine (T)), and the purines (adenine (A) and guanine (G)).
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Concept 2: DNA Double
Helix
DNA consists of two polynucleotide chains wound around each
other to form a double helix. The helix twists in the right-handed
direction—think of two strands of rope twisted around each other
in the clockwise direction. This twisting is an inherent property of
DNA, and it is the same when the helix is looked at from either end.
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The Polynucleotide Chain
DNA consists of two polynucleotide chains wound around each
other to form a double helix. Each polynucleotide chain
consists of a string of nucleotides linked by phosphodiester
bonds.
A DNA chain consists of nucleotides joined by bonds between phosphate and sugar (=
phosphodiester bonds). One end of the chain ends with a phosphate linked to the 5'
carbon of the sugar and is called the 5' end. The other end of the chain ends with an
hydroxyl group linked to the 3' carbon of the sugar and is called the 3' end.
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A Closer Look: Chemistry of a DNA
Polynucleotide Chain
In a DNA polynucleotide chain, nucleotides are joined by
phosphodiester bonds formed between the 5' carbon of one
sugar and the 3' carbon of the next sugar. A free phosphate
defines the 5' end of the chain and a free hydroxyl group defines
the 3' end of the chain.
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Complementary Base Pairing
DNA consists of two polynucleotide chains
wound around each other to form a double
helix. The two chains are held together by
complementary base pairing; that is, specific
bonding between A and T bases and between G
and C bases on the two strands.
To make a stable double helix, the two strands of DNA are
antiparallel; that is, the 5' → 3' direction of one strand runs
opposite to the other strand.
The two DNA chains are held together by complementary base
pairing between A and T bases and between G and C bases. Two antiparallel DNA
polynucleotide
chains held together
by complementary
base pairing.
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A Closer Look: Chemistry of
Complementary Base Pairing
Complementary base pairing involves specific hydrogen
bonding between A and T bases (two bonds) and between G
and C bases (three bonds).
Chemical structure of A-T and G-C base pairs in DNA.
In complementary base pairing, the two DNA chains are held together by hydrogen
bonds between A and T (two hydrogen bonds) and C and G (three hydrogen bonds).
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Concept 3:
Semiconservative Model of
DNA Replication
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Replicating DNA
After Watson and Crick proposed the double helix model of
DNA, three models for DNA replication were proposed:
conservative, semiconservative, and dispersive. The
semiconservative model was proved to be the correct one.
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Concept 4: Biosynthesis of
DNA
DNA polymerase catalyzes the synthesis of DNA using a
DNA strand as a template.
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BioSynthesis of DNA
DNA polymerase catalyzes the synthesis of DNA in the 5' to 3'
direction using a DNA strand as a template.
DNA polymerase catalyzes the synthesis of new DNA in the 5' to 3' direction using a DNA template
strand. The substrates for DNA polymerase are not the nucleotides but related molecules called
nucleoside triphosphates. Nucleoside triphosphates have three phosphate groups instead of the one
phosphate characteristic of nucleotides. In DNA biosynthesis, a nucleoside triphosphate base pairs
with the base on the DNA template strand, and a phosphodiester bond is formed between the
growing DNA chain and the new nucleotide. DNA polymerase both ensures that the correct base pair
is formed and catalyzes the formation of the phosphodiester bond.
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Concept 5: Replicating
Antiparallel DNA Strands
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Replicating Antiparallel DNA Strands
The two DNA strands are antiparallel, yet DNA polymerase can
only synthesize new DNA in the 5' to 3' direction. This poses
special problems for replicating double-stranded DNA.
The double-stranded DNA shown above is unwinding and ready for
replication. Note the antiparallel nature of the strands; that is, the 5' to 3'
orientation of the top strand and the 3' to 5' orientation of the
complementary bottom strand.
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How Antiparallel DNA Strands Are
Replicated
The two DNA strands are antiparallel, yet DNA polymerase can
only synthesize new DNA in the 5' to 3' direction. This poses
special problems for replicating double-stranded DNA.
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Concept 6: Enzymes and
Proteins in DNA
Replication
A large number of enzymes and other proteins are involved
in the synthesis of new DNA at a replication fork.
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Enzymes and Proteins in DNA
Replication
DNA polymerase
Location: On the template strands.
Function: Synthesizes new DNA in the 5' to 3' direction using the base information on the
template strand to specify the nucleotide to insert on the new chain. Also does some
proofreading; that is, it checks that the new nucleotide being added to the chain carries the
correct base as specified by the template DNA. If an incorrect base pair is formed, DNA
polymerase can delete the new nucleotide and try again. In E. coli the enzyme used for all new
DNA synthesis except for the replacement of the RNA primers is DNA polymerase III. DNA
polymerase I replaces the primers.
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Enzymes and Proteins in DNA
Replication
Another DNA polymerase
This DNA polymerase replaces the RNA primer with DNA. This is a different type of DNA
polymerase from the main DNA polymerase which synthesises DNA on a DNA template.
In E. coli the main enzyme is DNA polymerase III and the enzyme that replaces the RNA
primer with DNA is DNA polymerase I. When the RNA primer has been replaced with
DNA, there is a gap between the two Okazaki fragments and this is sealed by DNA ligase.
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Enzymes and Proteins in DNA
Replication
DNA ligase
DNA ligase seals the gap left between Okazaki fragments after the primer is removed. As
the Okazaki fragments are joined, the new lagging strand becomes longer and longer.
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Enzymes and Proteins in DNA
Replication
Helicase
Location: At the replication fork.
Function: Unwinds the DNA double helix.
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Enzymes and Proteins in DNA
Replication
Lagging Strand
The new DNA strand made discontinuously in the direction opposite to the direction in
which the replication fork is moving.
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Enzymes and Proteins in DNA
Replication
Leading strand
The new DNA strand made continuously in the same direction as movement of the
replication fork.
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Enzymes and Proteins in DNA
Replication
Okazaki fragment
Location: On the template strand which dictates new DNA synthesis away from the
direction of replication fork movement.
Function: A building block for DNA synthesis of the lagging strand. On one template
strand, DNA polymerase synthesizes new DNA in a direction away from the replication
fork movement. Because of this, the new DNA synthesized on that template is made in a
discontinuous fashion; each segment is called an Okazaki fragment.
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Enzymes and Proteins in DNA
Replication
Overall direction of replication (movement of replication fork)
The direction of replication i.e., the direction in which the replication fork moves as the
DNA double helix unwinds.
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Enzymes and Proteins in DNA
Replication
Parent DNA
The parental DNA double helix that will be unwound and used as the template for new
DNA synthesis.
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Enzymes and Proteins in DNA
Replication
Primase
Location: Wherever the synthesis of a new DNA fragment is to commence.
Function: DNA polymerase cannot start the synthesis of a new DNA chain, it can only
extend a nucleotide chain primer. Primase synthesizes a short RNA chain that is used as
the primer for DNA synthesis by DNA polymerase.
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Enzymes and Proteins in DNA
Replication
Single-strand binding (SSB) proteins
Location: On single-stranded DNA near the replication fork.
Function: Binds to single-stranded DNA to make it stable.
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