Introduction to Microbial Genetics by cp7R8FS8


									 Introduction to
Microbial Genetics

   Microbiology 221
A Historical Overview
The scientists who provided the clues to
            the nature of DNA
Friederich Meischer – DNA isolated
Luria and Delbruck – Bacteriophages
Stanely Giffiths( 1928) The idea of the
transforming “ substance” – Avery,
MacLoed, and McCarty( 1944) – the
nature of transformation
Hershey and Chase – Bacteriophage –
DNA as the hereditary material
Chargaff – A= T and C=G
Maurice Wilkins and Rosalind Franklin – x-
ray crystallography of DNA
Watson and Crick – Double helix
Luria and Delbruck at Cold
  Spring Harbor in 1953
Luria and Delbruck
   studied bacterial
   mutations and
   resistance to
   infection with
The characterized the
   virus and its life cycle
Alfred Hershey and Martha Chase
   and the Blender Experiment
Hershey and Chase
wanted to verify that
DNA was the
hereditary material
They used a
bacteriophage for
their study
They labeled the DNA
with Radioactive P(
P32) and the protein
with radioactive
sulfur( S35)
        Results of the
Proved that the radioactivity from the labeled
DNA was present in the progeny phage produced
from infection of the bacteria.
The Race for the Double
Rosalind Franklin
and Maurice
Wilkins at Kings
Studied the A and
B forms of DNA
Rosalind’s famous
picture of the B
form held the
secret, but she
didn’t realize its
The Race for the Double
Watson and Crick
formed an unlikely
A 22 year old PhD and
a 34 year old “want to
be” PhD
embarked on a model
making venture at
Used the research of
other scientists to
determine the nature
of the double helix
 Nucleic Acid Composition
      DNA and RNA
     DNA – Basic Molecules
a.   Purines – adenine and guanine
b.   Pyrmidines – cytosine and thymine
c.   Sugar – Deoxyribose
d.   Phosphate phosphate group - DNA background
            Double Helix
   Two polynucleotide strands joined by
   phosphodiester bonds( backbone)
   Complementary base pairing in the center of the
A= T and      C     G – base pairing. Two hydrogen
   bonds between A and T and three hydrogen bonds
   between C and G.
A purine is bonded to a complementary pyrimidine
   Bases are attached to the 1’ C in the sugar
   At opposite ends of the strand – one strand has
   the 3’hydroxyl, the other the 5’ hydroxyl of the
   sugar molecule
        DNA Structure - DNA
        Double helix
        ( continued)
The double helix is right handed – the
chains turn counter-clockwise.
As the strand turn around each other
they form a major and minor groove.
The is a distance of .34nm between each
The distance between two major grooves
is 2.4nm or 10 bases
The diameter of the strand is 2nm
Complementary Base
Adenine pairs
with Thymine
Cytosine pairs
with Guanine
The end view of DNA
This view shows
the double
helix and the
outer backbone
with the bases
in the center.
An AT base
pair is
highlighted in
 Double helix and anti-
  DNA is a directional molecule
  The complementary strands
  run in opposite directions
  One strand runs 3’-5’
  The other strand runs 5’ to 3’
( the end of the 5’ has the
  phosphates attached, while the
  3’ end has a hydroxyl exposed)
    RNA structure
Polynucleotide – nucleic acid -
Single stranded molecule that
can coil back on itself and
produce complementary base-
pairing ( t- RNA)
Four bases in RNA are Adenine
and Guanine ( purines) and
Cytosine and Uracil(
Sugar – ribose
     Three types of RNA
a.   Messenger
b.   Transfer
c.   Ribosomal
d.   nc- non coding RNA’s
    Prokaryote DNA
Tightly coiled
Coiling maintained by molecules
similar to the coiling in eukaryotes
Circular ds molecule
Borrelia burgdoferi ( Lyme Disease
)has a linear chromosome
Other bacteria have multiple
Agrobacterium tumefaciens (
Produces Crown Gall disease in
plants) has both circular and linear
Circular DNA
    E. coli – most often
   studied in molecular
 biologyE.of are located on a circular
The genes of coli
chromosome of 4.6 million basepairs. This 1.6
mm long molecule is compressed into a highly
organized structure which fits inside the 1-2
micrometer cell in a format which can still be
read by the gene expression machinery.
 Bacterial DNA is supercoiled by DNA gyrase.
Chemical inhibition of gyrase without allowing
the cells to reprogram gene expression relaxes
supercoiling and expands the nucleoid,
suggesting that supercoiling is one of the tools
used to compress the genome
Coiling maintained by Gyrase
Relaxation of the coils by
Nucleosome formation
DNA is more highly
organized in
eukaryote cells
The DNA is
associated with
proteins called
histones.( eukaryotes)
These are small basic
proteins rich in the
amino acids lysine
and/or arginine
There are five
histones in eukaryote
cells, H1, H2A,
H2B,H3 and H4.
   Beads on a String
The DNA coils around the ellipsoid
approximately 1 ¾ turns or 166 base pairs
before proceeding to the next.
The DNA + the histone proteins arranged
in this formation are referred to as a
The stretch of DMA between the beads
varies in length from 14 to 100 base pairs.
H1 appears to associate with the linker
regions to enable the nucleosome to
When folding of the structure reaches a
maximum, the chromosomes can be
Chromosome structure
Eukaryote replication
The nature of
replication was
elucidated by
Meselson and
        Meselson and Stahl
     Grew bacteria in heavy Nitrogen – N-15
2. Transferred bacteria to N-14
3. Before bacteria reproduce in new media, all bacteria
   contain heavy DNA
4. Samples were taken after one round of replication and
   two round of replication
Each original strand
serves a template or
pattern for the
replication of the new
The new strand
contains one original
and a newly
synthesized strand
Eukaryote replication
Multiple linear chromosomes
Each chromosome has more than one origin of
Approximately 1400 x as long as bacterial DNA
Multiple replicons on a chromosome
Oris along the length – every 10 to 100 um
Replication forks and bubbles are formed.
Replication proceeds bidirectionally until the
bubbles meet
This shortens the length of time necessary to
replicate eukaryote chromosomes
The process of elongation occurs at a speed of
50-100 base pairs/minute as compared to 750 to
1000 base pairs/ minute
The origin of replication
 and replication forks
Eukaryote replication
During the S phase, there are 100
replication complexes and each one
contains as many as 300 replication forks.
These replication complexes are
stationary. The DNA threads through
these complexes as single strands and
emerges as double strands.
   DNA Polymerases
Fourteen DNA polymerases
have been observed in human
beings as compared to three in
E. coli.
Prokaryote Replication
Enzyme                      Type          Source           Properties
Bacterial topoisomerase I                                  Relaxation of negative but
                             I            E. coli
(v protein)                                                not positive supercoils
Vaccinia virus                                             Relaxation of positive and
                             I        Vaccinia virus
topoisomerase I                                            negative supercoils
Eukaryotic topoisomerase                                   Relaxation of positive and
                             I         Calf thymus
I                                                          negative supercoils
                                                           Introduces positive
Reverse gyrase               I     Thermophilic bacteria
                                                           supercoils into DNA
                                    Hyperthermophilic      Relaxation of positive
Topoisomerase V              I
                                        bacteria           supercoils
                                                           Introduces negative
DNA gyrase                   II           E. coli
                                                           supercoils into DNA
                                                           DNA relaxation and
Topoisomerase IV             II           E. coli
                                                           potent decatenation
                                                           Relaxation of positive and
T4 topoisomerase II          II      Bacteriophage T4      negative supercoils and
                                                           Relaxation of positive and
Eukaryotic topoisomerase
                             II        S. cerevisiae       negative supercoils and
Bidirectional replication
 There is an origin
 of replication
 Two replication
 forks are formed
 Replication occurs
 around the circle
 until they have
 opened and copied
 the entire
 Replicon- contains
 an origin and is
 replicated as a
Ori – Origin of replication
 Characteristics used to define Origins:
 The position on the DNA at which replication
 start points (see right) are found.
 A DNA sequence that when added to a non-
 replicating DNA causes it to replicate.
 A DNA sequence whose mutation abolishes
 A DNA sequence that in vitro is the binding
 target for enzyme
When the double helix of DNA, which is
composed of two strands, separates,
helicase makes these two strands rotate
around each other.
The DnaB protein is the helicase most
involved in replication, but the n’ protin
may also participate in unwinding.
The single stranded binding proteins
SSBP help to keep the strand open
But there is a problem due to the
topological reason that the unreplicated
part ahead of the replication fork will
rotate around its helical axis when the
two strands separate at the replication
Topoisomerase action
It causes strong strain in the helix
(1). Thus, it is impossible to unlink
the double helical structure of
DNA without disrupting the
continuity of the strands.
In order to perform unraveling of a
"compensating winding up" DNA,
enzymes are required (1).
Topoisomerase changes the linking
number as well as catalyzes the
interconversionn of other kinds of
topological isomers of DNA (2).
a. oriC - origin of chromosomal replication
Recognized by DnaA protein - only
recognizes if GATC sites are fully
Binding of DnaA allows DnaB to open
b. DnaB is the replication helicase
c. Strand separation by helicase
d. SSB (single-stranded binding) protein
keeps strands apart
e. DNA gyrase - a topoisomerase - puts
swivel in DNA which allows strands to
rotate and relieve strain of unwinding

Recall that DNA double helix is tightly wound
structure and that bases lie between the two
backbones. If these bases are the template for
new strand, how do the appropriate enzymes
reach these bases? By the unwinding of the helix.

An enzyme called helicase catalyzes the unwinding
of short DNA segments just ahead of the
replication fork. The reaction is driven by the
hydrolysis of ATP.
Explanation continued
As soon as duplex is unwound, SSB
(single-stranded binding protein) binds to
each of the separated strands to prevent
them from base-pairing again. Therefore,
the bases are exposed to the replication

The unwinding of the duplex would cause
the entire DNA molecule to swivel except
for the action of a topoisomerase (DNA
gyrase) which introduce breaks in the
DNA just ahead of the unwinding duplex.
These breaks are then rejoined after a
few revolutions of the duplex.
The need for a primer

When DNA template is exposed, DNA
synthesis must begin. But DNA
polymerases not only need a template but
also a primer for replication to proceed.
Where does the primer come from?
After observations that RNA synthesis is
required for DNA synthesis, it was
discovered that the synthesis of DNA
fragments requires a short length of
RNA as a primer.
Primosome (complex of 20 polypeptides)
makes RNA primers in E. coli
Formation of the Primer
Primosome contains primase
Primosome moves along DNA duplex in
3'>5' direction (with respect to lagging
strand; follows replication fork) even
though primer is made in 5'>3' direction
(Note: The symbol ">" indicates the
direction; that is, the primer is made
from 5' to 3'.)
n' protein removes SSB in front of
DnaB protein organizes some components
of primosome and prepares DNA for
Primase forms the primer
Complex that
synthesizes most of the
DNA copy contains the
DNA polymerase enzyme
and other proteins
The gamma delta
complex and the B
subunits of the
holoenzyme bind it to
the template and the
The alpha subunit
carries out the actual
polymerization reaction
All of the proteins form
a huge complex called
the replisome
DNA polymerase III
This is a
complex that
attached to the
The DNA moves
through the
replisome and is
  Elongation of the chain
  dCMP +
  Energy is
  supplied for
  biosynthesis by
  the cleaving of
  the phosphate
Elongation( continued)
Elongation proceeds in 5' > 3'
direction and requires
1) all 4 deoxyribonucleoside 5'-
triphosphates (dATP, dGTP, dCTP,
2) Mg+ ions,
3) a primer made of nucleic acid,
4) a DNA template.

Rate of elongation = 750 - 1000
nucleotides per second
Rate of formation of initiation
complex = 1-2 minutes
DNA polymerase I, II and III in E .coli
DNA polymerase III holoenzyme - complex of 7

Replisome - primosome and 2 DNA polymerase III -
synthesizes DNA on both strands simultaneously
without dissociating from DNA

DNA polymerase III catalyzes the addition of
deoxyribonucleotide units to end of the DNA strand
with release of inorganic pyrophosphate (PPi)
(DNA)n residues + dNTP <-> (DNA)n + 1 residues + PPi
Attachment of new units is by their a-phosphate groups
to a free 3'-hydroxyl end of preexisting DNA chain.
 The lagging strand and
discontinuous replication
The replication on the 5’ to 3’ strand
The template strand still must be read
from 3’ to 5’
The reading begins at the replication fork
Occurs at the same time as the synthesis
of the lagging strand
Same steps in synthesis of DNA
But DNA is synthesized in pieces about
1000 to 2000 bases in length. These are
known as Okazaki fragments
    Okazaki fragments
  After the lagging strand has been
  duplicated by the formation of Okazaki
  fragments, DNA Polymerase I or RNase
  H removes the RNA primer. Polymerase I
  synthesizes the complementary DNA to
  fill the gap resulting from the RNA

 The polymerase removes one nucleotide
 at a time and then replaces it
AMP( RNA nucleotide) replaced by dAMP(
 DNA nucleotide)
           DNA ligase
Ligase can catalyze
the formation of a
phosphodiester bond
given an unattached
but adjacent 3'OH
and 5'phosphate.
This can fill in the
unattached gap left
when the RNA primer
is removed and filled
The DNA polymerase
can organize the bond
on the 5' end of the
primer, but ligase is
needed to make the
bond on the 3' end.
The End of Replication
DNA replication stops when the
polymerase complex reaches a
termination site on the DNA in E. coli
The Tus protein binds to the ter site and
halts replication.
In many prokaryotes the replication
process stops when the replication forks
   Plasmid replication
ColE1 is a naturally occurring plasmid of E. coli.
Its replication is controlled independently of the
replication of the host chromosome.
Two plasmids with the same origin of replication
can not coexist in the same cell.
The ColE1 origin, defined by molecular genetic
methods, is in a region from which two RNAs are
An active RNase H gene is required for ColE1
replication. RNase H cleaves the RNA II
transcript. The remaining RNA serves as primer
for initiation of replication.
RNA I binds to 5' sequences of RNA II via
pseudoknots and regular complementary pairing.
This binding is stabilized by the ROP or ROM
The binding prevents changes in the conformation
of RNA II that would otherwise result in RNAse
H cleavage.
Rolling Circle Replication – Occurs in
Conjugation in E. coli.
How can one account for the high fidelity of

   The answer is based on the fact that DNA
  Polymerase absolutely requires 3'-OH end of
  base-paired primer strand on which to add new

  DNA polymerase III has 3' > 5' exonuclease
  activity. It was discovered that DNA polymerase
  III actually proofreads the newly synthesized
  strand before continuing with replication. When
  incorrect nucleotide is incorporated, DNA
  polymerase III, by means of the 3' > 5'
  exonuclease activity, "backs up" and hydrolyzes
  off the incorrect nucleotide. The correct
  nucleotide is then added to the chain and
  elongation is resumed.

  All 3 DNA polymerases have 3'>5' exonuclease

  Proofreading ability - 1 error in 10 million
Exonucleases and repair
 DNA polymerase I also has 5'>3'
 exonuclease activity which removes RNA
 primer and 5'>3' polymerase activity
 which fills in the gap

 This causes a single-stranded break in
 the DNA - called a nick
 DNA ligase repairs nick by creating a
 phosphodiester bond
        Genes and Gene
Genes are written in a code consisting of groups of three
letters called triplets.
There are four letters in the DNA alphabet. There are 64
possible arrangements of the four letters in groups of three
The triplets specify amino acids for the synthesis of proteins
from the information contained in the gene
Genes can also specify t- RNA or r- RNAs
The gene begins with a start triplet and ends with a stop. The
bases between the start and the stop are called an open
reading frame, ORF.
The information in the gene is transcribed by RNA
It reads the gene from 3’ to 5’
The template strand is now referred to as the CRICK strand
and the nontemplate strand is now known as the WATSON
DNA sequences are stored in data bases as the WATSON
        Reference - COLD SPRING HARBOR - 2003
Promoters are at the beginning of the
   RNA polymerase recognizes a binding site in front
   of the gene. This is referred to as upstream of
   the gene.
   The direction of transcription is referred to as
   Different genes have different promoters. IN E.
   coli the promoters have two functions
   The RNA recognition site for transcription which
   is the consensus sequence for prokaryotes is
5’ TTGACA3’ ( Watson strand) which means on the
   reading strand 3’ AACTGT5’ ( Crick strand)
  The Pribnow Box and Shane -
   The RNA binding site has a consensus sequence of
5’ TATAAT 3’ ( -) and 3’ ATATTA 5’ (+)
   This is where the DNA begins to become unwound
   for transcription
   The initially transcribed sequence of the gene
   may not reflect doing but may be a leader
   The prokaryotes usually contain a consensus
   sequence known as the Shane Delgarno which is
   complememtary to the 16s rRNA on the ribosome
   ( small subunit )
   The leader sequence also may regulate
The structure of a
 prokaryote gene
Prokaryote Genes are
They do not contain introns like
eukaryote genes
The gene consists of codons that will
determine the sequence of amino acids in
the protein
At the end of the gene there is a
terminator sequence rather than an
actual stop
The terminator may be at the end of a
trailer sequence located downstream
from the actual coding region of the gene
The Gene begins with
DNA is read 3’ to 5’ and m RNA is
synthesized 5’ to 3’
3’ TAC is the start triplet
This produces a complementary
mRNA message 5’ AUG 3’ –
Groups of three bases in the
messenger RNA formed are
referred to as CODONS
•There is wobble in
the DNA code – This
is a protection from
•More than one codon
can specify the same
amino acid
• Note arginine -
all code for arginine –
only the third base in
the codon changes
•There are two
additional codons for
arginine as well AGA
and AGG these
reflect the
degenerate nature of
the code
Codon chart
Genes for t RNAs and r
The genes for t RNAs have a
promoter and transcribed leader
and trailer sequence that are
removed prior to their utilization in
translation. Genes coding for tRNA
may code for more than a single
tRNA molecule
The segments coding for r RNAs
are separated by spacer sequencs
that are removed after
The acceptor stem
includes the 5' and 3'
ends of the tRNA.
The 5' end is
generated by RNase P
The 3' end is the site
which is charged with
amino acids for
Aminoacyl tRNA
synthetases interact
with both the
acceptor 3' end and
the anticodon when
charging tRNAs.
The anticodon
matches the codon on
mRNA and is read
3’ to 5’
         t- RNA
Found in the cytoplasm
Amino acyl t- RNA synthetase
is an enzyme that enables the
amino acid to attach to t-RNA
Also activates the t- RNA
Clover leaf has a stem for
attachment to the amino acid
and an anticodon on the bottom
of the clover leaf
               t- RNA
Common Features
  a CCA
  trinucleotide at
  the 3' end,
  four base-paired
  stems, and
  One loop
  containing a T-
  sequence and
  another containing
tRNAs attach to a
specific amino
acid and carry it
to the ribosome
There are 20
amino acids
61 different
codons for these
amino acids and 61
The anticodon is
complementary to
the codon
Binds to the codon
with hydrogen
    Ribosomal genes

Very similar to the structure of
protein genes
tRNA and rRNA genes
The genes for rRNA are also similar to the
organization of genes coding for proteins
All rRNA genes are transcribed as a large
precursor molecule that is edited by
ribonucleases after transcription to yield the
final r RNA products
    Ribosomal RNA
Combines with specific
proteins to form ribosomes
Serves as a site for protein
Associated enzymes and
factors control the process of
Prokaryote ribosomes
Ribosomes are small, but
complex structures,
roughly 20 to 30 nm in
diameter, consisting of
two unequally sized
subunits, referred to as
large and small which fit
closely together as seen
 A subunit is composed
of a complex between
RNA molecules and
proteins; each subunit
contains at least one
ribosomal RNA (rRNA)
subunit and a large
quantity of ribosomal
The subunits together
contain up to 82 specific
proteins assembled in a
precise sequence.
Prokaryote ribosomal RNA

 Type of                  Subunit
           e number of
  rRNA                    Location

   16s        1,542         30s

   5s          120          50s

   23s        2,904         50s
 Prokaryote ribosomes –
polysomes- the process of
Prokaryote transcription
    and translation
Prokaryote transcription and
translation take place in the
All necessary enzymes and
molecules are present for the
transcription and translation to
take place

 A molecule of messenger RNA
 binds to the 30S ribosome
( small ribosomal unit) at the
 Shine Dalgarno sequence
 This insures the correct
 orientation for the molecule
 The large ribosomal sub unit
 locks on top
       The Ribosome

There are four significant
positions on the ribosome
When the 5’ AUG 3’ of the
mRNA is on the P site the t-
RNA with the anticodon,
5’UAG3’ forms a temporary
bond to begin translation
From Gene to
E. Coli Gene Map
   Mutations in DNA
May be characterized by their
genotypic or phenotypic change
Mutations can alter the phenotype
of a microorganisms in different
Mutations can involve a change in
the cellular or colonial morphology
    Types of Mutations
   Conditional mutations are those mutations
   that are expressed only under specific
   environmental conditions ( temperature)
   Biochemical mutations are those that can
   cause a change in the biochemistry of the
( these may inactivate a biochemical
These mutants are referred to as
   auxotrophs because they cannot grow on
   minimal media
Prototrophs are usually wild type strains
   capable of growing on minimal media
Two types of mutations
Spontaneous mutations – These
occur without a causative agent
during replication
Induced mutations are the result
of a substance referred to as a
Cairns reports that a mutant E. coli
strain unable to use lactose is able
to regain its ability to use the
sugar again – should this be
referred to as adaptive mutation?
One possible explanation is
A starving bacterium has the
ability to generate multiple
mutations with special mutator
genes that enable them to
form bacteria with the ability
to metabolize lactose
This is an interesting theory
still under investigation
 Spontaneous mutations
1.  A purine substitutes for a purine or a
    pyrimidine substitutes of a pyrimidine. This
    type of mutation is referred ta as a transition.
    Most of these can be repaired by proofreading
2.  A pyrimidine substituted for by a purine is
    referred to as a transversion. These are rarer
    due to steric problems in the DNA molecule
    such as pairing purines with purines.
3.  Insertions or deletions cause frame shifts –
    the code shifts over the number of bases
    inserted or deleted
      Mutation Types
Erors in replication
due to base
AT and CG pairs are
formed when keto
groups participate in
hydrogen bonds
In contrast enol
tautomers produce AC
and GT base pairing
Spontaneous mutations –
    another cause
A purine nucleotide can lose its
It will not base pair normally
It will probably lead to a
transition type mutation after
the next round of replication.
Cytosine can be deaminated to
uracil which can then create a
       Frame Shifts
Additions and
deletions change
the reading frame.
The hypothetical
origin of deletions
and insertions may
occur during
If the new strand
slips an insertion
or addition may
If the parental
slips a deletion
may occur
     Any agent that
     directly damages
     DNA, alters its
     chemistry, or
     interferes with
     repair mechanisms
     will induce mutations
a.   Base analogs
b.   Specific mispairing
c.   Intercalating agents    Base analogs are structurally
d.   Ionizing radiation      similar to normal nitrogenous
                             bases and can be
                             incorporated into the
                             growing polynucleotide chain
                             during replication.
  The expression of
Forward mutations – a mutation
from the wild type to a mutant
form is called a forward mutation
Reversion-If the organism regains
its wild type characteristics
through a second mutation
Back mutation – The actual
nucleotide sequence is converted
back to the original
Suppressor mutation – overcomes
the effects of the first mutation
  More on mutations
Point mutations – caused by the
change in one DNA base
Silent mutations – mutations can
occur which cause no effect – this
is due to the degeneracy of the
code ( more than one base coding
for the same amino acid)
Missense mutation – changes a
codon for one amino acid into a
codon for another amino acid
Nonsense – In eukaryotes the
substitution of a stop into the
sequence of a normal gene
Detection and isolation of
 Requires a sensitive system
 Mutations are rare
 One in about every 107 – 1011
 Replica plating is a technique that is used
 to detect auxotrophs
 It distinguishes between wild type and
 mutants because of their ability to grow
 in the absence of a particular
 biosynthetic end product
 Replica plating allows plating on minimal
 media and enriched media from the same
 master plate
    The selection of
  auxotorph revertants
The lysine auxotrophs
( Lys-) are treated
with a mutagen such
as nitroquanidine or
uv light to produce
       Ames Test
Developed by Bruce Ames
Used to test for carcinogens
A mutational reversion assay
based upon mutants of
Salmonella typhimurium
DNA repair mechanisms
Type I -Excision repair
Corrects damage which causes distortions in the
  double helix
  A repair endonuclease or uvr ABC endonuclease
  removes the damaged bases along with some
  bases on either side of thee lesion
  The usual gap is about 12 nucleotides long. It is
  filled by DNA polymerase and ligase joins the
  This can remove Thymine-Thymine dimers
  A special type of repair utilizes glycosylases to
  remove damaged or unnatural bases yielding the
  results discussed above
   Mutations and repair
Type II – Removal of lesion
    Thymine dimers and alkylated bases are often
    repaired directly
    Photoreactivation is the repair of thymine
    dimers by splitting them apart into separate
    thymines with the aid of visible light in a
    photochemical reaction catalyzed by the
    enzyme photolyase
    Light repair
    -phr gene - codes for deoxyribodipyrimidine
    photolyase that, with cofactor folic acid, binds
    in dark to T dimer. When light shines on cell,
    folic acid absorbs the light and uses the energy
    to break bond of T dimer; photolyase then falls
    off DNA
        Dark repair of
Dark repair
Three types
1) UV Damage Repair (also called NER - nucleotide
excision repair)
Excinuclease (an endonuclease; also called
correndonuclease [correction endo.]) that can
detect T dimer, nicks DNA strand on 5' end of
dimer (composed of subunits coded by uvrA, uvrB
and uvrC genes).
UvrA protein and ATP bind to DNA at the
UvrB binds to the UvrA-DNA complex and
increases specificity of UvrA-ATP complex for
irradiated DNA.
UvrC nicks DNA 8 bases upstream and 4 or 5
bases downstream of dimer.
UvrD (DNA helicase II; same as DnaB used during
replication initiation) separates strands to release
12-bp segment.
DNA polymerase I now fills in gap in 5'>3'
direction and ligase seals.
The Effects of uv light
Post replication repair
If T dimer not repaired, DNA Pol III can't make
complementary strand during replication.
Postdimer initiation - skips over lesion and leaves
large gap (800 bases). Gap may be repaired by
enzymes in recombination system - lesion remains
but get intact double helix.
Successful post replication depends upon the
ability to recognize the old and newly replicated
DNA strands
This is possible because the newly replicated DNA
strand lack methyl groups on their bases, whereas
the older DNA has methyl groups on the bases of
both strands.
The DNA repair system cuts out the mismatch
from the non- methylated strand
Recombination repair
The DNA repair for which there is no remaining
template is restored
RecA protein cuts a piece of template DNA from
a sister molecule and puts it into the gap or uses
it to replace a damaged strand
Rec A also participates in a type of inducible
repair known as SOS repair.
If the DNA damage is so great that synthesis
stops completely leaving many gaps, the Rec A will
bind to the gaps and initiate strand exchange.
It takes on a proteolytic funtion that destroys
the lexA repressor protein which regulates genes
involved in DNA repair and synthesis

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