DNA replication (BOOK)
Chapter 5 pp 237-254
DNA replication, repair and recombination
The maintenance of DNA sequences
Mutations, which are permanent changes in the DNA only occur rarely. The rate at which changes
occur in the DNA is called the mutation rate and is very low. The fraction of damaged genes
underestimates the actual mutation rate because many mutations are silent.
The cells of a sexual reproducing animal are of two types, germ cells and somatic cells. Germ cells
must be protected against high rates of mutations to maintain the species. However the somatic cells
should be protected to to properly maintain the organised structure of the body.
DNA replication mechanisms
DNA templating is the mechanism the cell uses to copy the nucleotide sequence of one DNA strand
into a complementary DNA sequence. This requires the DNA helix to separate into two template
strands. The separation exposes the hydrogen bonds for base pairing with the appropriate free
nucleotide. This nucleotides are added by an enzyme called DNA polymerase. The growth direction is
from the 5’end to the 3’end (so from the 3’end to the 5’end out of perspective of the template
strand).
Replication fork
When the DNA helix is separated, there are two strands that can be replicated. These two strands are
replicated at the same time. A daughter cell will also inherit a new DNA double helix with one original
and one new strand, therefore the DNA double helix is said to be replicated ‘’semiconservatively’’.
The replication fork is the active region where the DNA is separated and replicated.
, Because of the antiparallel orientation of the two DNA strands in the double helix, one daughter
strand would be polymerised in the 5’-to-3’ direction and the other in the 3’-to-5’ direction.
However, the DNA polymerase can only synthesise in the 5’-to-3’ direction.
The strand which can’t be replicated is replicated by another mechanism including Okazaki
fragments. These fragments are about 100-200 nucleotides long, and are pasted in the 5’-to-3’ end
direction. The strand which can be synthesised continually is called the leading strand while the
other strand is called the lagging strand.
Proofreading mechanisms
There are some proofreading mechanisms to avoid nucleotides being placed
incorrectly. One is done by the DNA polymerase which can ‘feel’ whether the
attraction between the nucleotides is correct. After the nucleotide binding to
the polymerase (specific nucleotides bind better to specific DNA
polymerases) the polymerase undergoes a conformational change in which is
shape is tightened around the active site. This change occurs more when the
nucleotides fit together, so this functions as a double-check for the DNA
polymerase.
The next error-correcting reaction is known as exonucleolytic proofreading
takes place after an incorrect nucleotide is covalent added to the growing
chain. This is done when a nucleotide is incorrectly bonded at the primer
strand. The primer strand is the beginning point for the DNA polymerase.
When the 3’-OH end of the primer isn’t correct the polymerase cant
continue. For illustration see picture right.
In case DNA polymerase added deoxyribonucleotide triphosphates in the 3’-
to-5’ direction instead of the 5’-to-3’ direction, the growing 5’ end of the
chain rather than the incoming nucleotide would provide the triphosphate.
In this case, mistakes in polymerisation can not be hydrolysed away because
the bare 5’end would terminate DNA synthesis.
Primers
For the leading strand a primer is only needed at
the start of replication. In contrast, on the lagging
strand, a primer is needed each time a DNA
polymerase has finished a short DNA Okazaki
fragment.
DNA primase is the enzyme which synthesizes short
RNA primers on the lagging strand. In eukaryotes
these primers are about 10 nucleotides long.
These DNA primers are replaced by DNA and the
holes between the Okazaki fragments are filled by
DNA ligase.
Chapter 5 pp 237-254
DNA replication, repair and recombination
The maintenance of DNA sequences
Mutations, which are permanent changes in the DNA only occur rarely. The rate at which changes
occur in the DNA is called the mutation rate and is very low. The fraction of damaged genes
underestimates the actual mutation rate because many mutations are silent.
The cells of a sexual reproducing animal are of two types, germ cells and somatic cells. Germ cells
must be protected against high rates of mutations to maintain the species. However the somatic cells
should be protected to to properly maintain the organised structure of the body.
DNA replication mechanisms
DNA templating is the mechanism the cell uses to copy the nucleotide sequence of one DNA strand
into a complementary DNA sequence. This requires the DNA helix to separate into two template
strands. The separation exposes the hydrogen bonds for base pairing with the appropriate free
nucleotide. This nucleotides are added by an enzyme called DNA polymerase. The growth direction is
from the 5’end to the 3’end (so from the 3’end to the 5’end out of perspective of the template
strand).
Replication fork
When the DNA helix is separated, there are two strands that can be replicated. These two strands are
replicated at the same time. A daughter cell will also inherit a new DNA double helix with one original
and one new strand, therefore the DNA double helix is said to be replicated ‘’semiconservatively’’.
The replication fork is the active region where the DNA is separated and replicated.
, Because of the antiparallel orientation of the two DNA strands in the double helix, one daughter
strand would be polymerised in the 5’-to-3’ direction and the other in the 3’-to-5’ direction.
However, the DNA polymerase can only synthesise in the 5’-to-3’ direction.
The strand which can’t be replicated is replicated by another mechanism including Okazaki
fragments. These fragments are about 100-200 nucleotides long, and are pasted in the 5’-to-3’ end
direction. The strand which can be synthesised continually is called the leading strand while the
other strand is called the lagging strand.
Proofreading mechanisms
There are some proofreading mechanisms to avoid nucleotides being placed
incorrectly. One is done by the DNA polymerase which can ‘feel’ whether the
attraction between the nucleotides is correct. After the nucleotide binding to
the polymerase (specific nucleotides bind better to specific DNA
polymerases) the polymerase undergoes a conformational change in which is
shape is tightened around the active site. This change occurs more when the
nucleotides fit together, so this functions as a double-check for the DNA
polymerase.
The next error-correcting reaction is known as exonucleolytic proofreading
takes place after an incorrect nucleotide is covalent added to the growing
chain. This is done when a nucleotide is incorrectly bonded at the primer
strand. The primer strand is the beginning point for the DNA polymerase.
When the 3’-OH end of the primer isn’t correct the polymerase cant
continue. For illustration see picture right.
In case DNA polymerase added deoxyribonucleotide triphosphates in the 3’-
to-5’ direction instead of the 5’-to-3’ direction, the growing 5’ end of the
chain rather than the incoming nucleotide would provide the triphosphate.
In this case, mistakes in polymerisation can not be hydrolysed away because
the bare 5’end would terminate DNA synthesis.
Primers
For the leading strand a primer is only needed at
the start of replication. In contrast, on the lagging
strand, a primer is needed each time a DNA
polymerase has finished a short DNA Okazaki
fragment.
DNA primase is the enzyme which synthesizes short
RNA primers on the lagging strand. In eukaryotes
these primers are about 10 nucleotides long.
These DNA primers are replaced by DNA and the
holes between the Okazaki fragments are filled by
DNA ligase.
