Bachelors Degree Biology ( DNA structure, replication and repair) Mind Map on DNA structure, replication and repair, created by Natalina Laria on 27/05/2016.
Common mechanisms for storage, replication and expression of genetic information suggest a single
origin for all life however, differences in detail are significant, especially between prokaryotes and
eukaryotes
Prokaryotic and eukaryotic cells
Prokaryotes have no nucleus Prokaryotes carry less DNA Prolaryotes do not have membrane bound
organelles Prokaryotes usually have 1 circular bacterial chromosome - eukaryotes usually have
multiple linear DNA chromosomes Prokaryotes not complexed by histones Prokaryotic cell diameter
is relatively small
DNA structure and organisation
Must be stable and protected
to store genetic
information
to prevent damage
(mutation)
Must be accessible
information can be
used to produce
functional cells
Native DNA is a
double helix of
complementary
antiparallel chains
Linked by
hydrogen
bonds
between
the bases
3 H bonds in a
G-C pair and 2
H bonds in an
A-T pair
Supercoiling of DNA
Separating the
two strands of
the DNA double
helix causes
supercoiling
Regulated by Topoisomerases and Gyrases
DNA packing
Nucleosomes
Small regions
of DNA are
wrapped
around
protein cores
Look like 'beads on a string'
an octamer of two copies of each of
the histones H2A, H2B, H3 and H4
(the nucleosomal histones)
Histones are
positively
charged
proteins.
Histone H1 binds outside the
nucleosome and has a
structural role
Role of DNA packing
DNA is safely stored but easy to access for
transcription and replication
DNA replication
DNA synthesis occurs in the 5’ to 3’ direction
leading strand is replicated continuously
lagging strand is replicated discontinuously
Okazaki fragments
RNA primer of each Okazaki fragment is replaced with
DNA and the adjacent fragments are joined by DNA ligase
DNA synthesis occurs in the
opposite direction to movement
of the replication fork
Nucleoside triphosphates are the substrates for DNA synthesis; pyrophosphate is released and the
nucleoside monophosphate is joined onto the growing strand
Initiation of DNA
replication requires
many different proteins
Initiator proteins
Recruits the rest of the
replication machinery
Helicase
Separates the two strands of
the double helix (breaks
hydrogen bonds)
Topoisomerase (gyrase)
Relieves supercoiling of DNA by
breaking backbone (covalent
bonds)
Topoisomerase inhibitors
Prevent DNA replication
Blocks topoisomerase I so that supercoils accumulate ahead of the
replication fork, preventing DNA replication
Single stranded binding protein
In a single stranded region of DNA where short regions of base paired
'hairpins' have been formed single stranded binding protein works to
straighten the strand through cooperative protein binding
Initiated at origins
Specific DNA sequence (Usually AT-rich)
Origin sequences bound
by DNA binding proteins
(initiator proteins)
Proceeds bidirectionally
Elongation requires
many different proteins
Primase
Primase is recruited to the origin when
the strands have been separated by
helicase
Primers are laid down 5’ to 3’ on both strands
(bidirectional replication)
DNA polymerases
DNA polymerase III
Main replication polymerase
Primer extension
Coordination of leading and
lagging strand synthesis
The two molecules of DNA pol III (one on each strand)
interact to ensure the two strands replicate together
DNA polymerase I
Replaces RNA primers with DNA
Exonuclease activity 5’ to 3’ - One nucleotide at a time is removed from
the 5’ end of the primer as one is added to the 3’ end of the preceding
Okazaki fragment (DNA synthesis 5’ to 3’)
Can back up and remove
incorrectly paired bases
use a 3’ to 5’ exonuclease activity to
remove incorrect bases
The 3’ end is then extended again as usual
In eukaryotes
DNA pol e on the leading strand and on the
lagging strand DNA pol d
High fidelity (proof-reading)
enzymes
DNA ligase
Seals the nick between two
Okazaki fragments
Nucleases - Enzymes that
cut nucleic acids (DNA or
RNA)
Exonuclease – cuts off one nucleotide at
a time from the end of a DNA molecule
Endonuclease – cuts internally in a DNA molecule
(may be sequence specific)
Replication errors and mismatch repair
Mismatch repair
operates soon after replication and distinguishes the
newly replicated strand (carrying the incorrect base) from
the parental, correct strand
Mismatch repair assumes that the parental strand is correct
Newly synthesised DNA is methylated but not immediately so Mismatch
repair acts on the non-methylated strand, soon after DNA replication
Hereditary non-polyposis colon cancer (HNPCC) is
due to inherited defects in mismatch repair genes
Replication strand slippage
misalignment of the template and newly synthesised
strand and results in unequal daughter strands
Replication of chromosome
ends
The last RNA primer on the
lagging strand cannot be replaced
Chromosomes have
repeated sequences at each
end, called telomeres
G-rich (on strand
with its 3’ end at
the chromosome
end)
Short repeats (6-10 bp)
Telomerase
Reverse transcriptase
enzyme that uses an RNA template to
make a complementary DNA strand
an enzyme
that
extends
chromosome
ends
by
adding
telomere
repeat
sequences.
Extends DNA so that strand remains same
size (fills in gap left by lost rna polymerase)
Mutation and DNA repair
Mutations
in germ cells will be passed on to offspring
in somatic cells may cause cancer
Mutations that disrupt regulation of cell division
may lead to cancer
Base mismatches
Base excision repair
the first step is
removal of the
base
Incorrect/modified bases are
recognised; different errors are
recognised by different glycosylases
A uracil specific
glycosylase
removes uracil in
the first step.
This is why DNA contains Thymine. It
makes the repair system able to
distinguish a problem much more
easily
Deamination changes base pairing
properties. This occurs
spontaneously but the rate can be
increased by some chemicals
Can lead to
point
mutations
Causes of mutation
Replication errors
Mispairing
or small
insertions
and
deletions
Spontaneous
chemical change to
DNA
Chemical mutagens
Radiation
UV light causes pyrimidine
dimers to form – usually
thymine
A single unrepaired thymine dimer can be lethal
because progress of high fidelity DNA polymerases is
blocked
Photoreactivation:
direct
repair
Not present in humans
An enzyme (photoreactivating enzyme) uses energy from
visible light to break the bonds between the two
pyrimidine residues
Direct repair involves
reversing the chemical
reaction causing the
DNA damage
Photolyase (or
photoreactivating enzyme)
splits the dimer to regenerate
normal DNA
Nucleotide excision repair
Detects and repairs bulky lesions in DNA,
eg thymine dimers and modified bases
1. Recognition of damage 2. Single strand binding
protein binds 3. Endonuclease cuts out damaged
region 4. New DNA synthesised
Translesion synthesis
Bases are randomly
incorporated opposite
the lesion (commonly A)
error-prone mechanism
that introduces mutations
New strand is
complete but likely to
carry a mutation
May leave pyrimadine dimer
unrepaired leading to cell
death
Bypasses the blockage of
DNA replication
Double-stranded DNA breaks
Repaired by Homologous
recombination or Nonhomologous
end-joining
Homologous recombination results in
exchange of genetic information
between homologous chromosomes
Recombination provides a
means to generate new
combinations of genes
generates genetic diversity
Blocks of genes are exchanged
between homologous
chromosomes
Can be used as
a repair system
When there is a Double
stranded break on one
chromosome The other is
used as a template for
repair, resulting in exchange
of genetic material
Nonhomologous end-joining Protein recognise
broken chromosomes and join the ends together
(no base pairing involved)
Error prone
Wrong ends could be
joined, causing
translocations