Replication, transcription,
translation and expression of
nucleic acid
Central dogma of molecular biology
replication
transcription
DNA
RNA
translation
PROTEIN
Solid arrow indicate types of information transfers that occur in cells. DNA
directs its own replication to produce new DNA molecule; DNA is transcribes
into RNA; RNA is translated into protein. The dashed lines represent
information transfers that occur in certain organisms.
Information Flow
DNA
RNA
Protein
Replication: DNA duplicates itself
Transcription: RNA is made on a DNA
template
Translation: Protein is synthesized
from AAs and the three RNAs.
Reverse Transcription: RNA directs
synthesis of DNA
RNA replication: RNA replicates itself

DNA replication is an anabolic polymerization process,
that allows a cell to pass copies of its genome to its
descendants.

The key to DNA replication is the complementary
structure of the two strands:

Adenine and guanine in one strand bond with thymine
and cytosine, respectively, in the other.
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DNA replication is a simple concept - a cell separates the
two original strands and uses each as a template for the
synthesis of a new complementary strand.
Biologists say that DNA replication is semiconservative
because each daughter DNA molecule is composed of
one original strand and one new strand.
Processes in DNA Replication
Initial Processes in DNA
Replication

DNA replication begins at a specific sequence of nucleotides called an origin.

First, a cell removes chromosomal proteins, exposing the DNA helix.
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Next, an enzyme called DNA helicase locally "unzips" the DNA molecule by breaking
the hydrogen bonds between complementary nucleotide bases, which exposes the
bases in a replication fork. Other protein molecules stabilize the single strands so that
they do not rejoin while replication proceeds
After helicase untwists and separates the strands, a molecule of an enzyme called
DNA polymerase III binds to each strand.
DNA polymerases replicate DNA in only one direction - 5' to 3' - like a jeweler
stringing pearls to make a necklace, adding them one at a time, always moving from
one end of the string to the other.
Because the two original (template) strands are antiparallel cells synthesize new
strands in two different ways. One new strand, called the leading strand, is
synthesized continuously as a single long chain of nucleotides.
The other new strand, called the lagging strand, is synthesized in short segments that
are later joined.
Synthesis of the Leading Strand
A cell synthesizes a leading strand toward the replication fork in the
following series of five steps
1) An enzyme called primase synthesizes a short RNA molecule that is
complementary to the template DNA strand. This RNA primer
provides the 3' hydroxyl group required by DNA polymerase.
2) Triphosphate deoxyribonucleotides form hydrogen bonds with their
complements in the parental strand. Adenine nucleotides bind to
thymine nucleotides, and guanine nucleotides bind to cytosine
nucleotides.
3) Using the energy in the high-energy bonds of the triphosphate
deoxyribonucleotides, DNA polymerase III covalently joins them one
at a time by dehydration synthesis to the leading strand.
4) DNA polymerase III also performs a proofreading function. About one
out of every 100,000 nucleotides is mismatched with its template; for
instance, a guanine might become incorrectly paired with a thymine.
DNA polymerase III recognizes most such errors and removes the
incorrect nucleotides before proceeding with synthesis. This role,
known as the proofreading exonuclease function, acts like the delete
key on a keyboard, removing the most recent error.
Because of this proofreading exonuclease function, only about one
error remains for every ten billion (1010) base pairs replicated.
5) Another DNA polymerase - DNA polymerase I - replaces the RNA
primer with DNA. Note that researchers named DNA polymerase
enzymes in the order of their discovery, not the order of their actions.
Synthesis of the Lagging Strand

The steps in the synthesis of a lagging strand are as follows

As with the leading strand, primase synthesizes RNA primers.

Nucleotides pair up with their complements in the template-adenine with
thymine, and cytosine with guanine.
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DNA polymerase III joins neighboring nucleotides and proofreads. In
contrast to synthesis of the leading strand, however, the lagging strand is
synthesized in discontinuous segments called Okazaki fragments. Each
Okazaki fragment requires a new RNA primer and consists of 1000 to
2000 nucleotides.

DNA polymerase I replaces the RNA primers of Okazaki fragments with
DNA and further proofreads the daughter strand.

DNA ligase seals the gaps between adjacent Okazaki fragments to form a
continuous DNA strand.
TRANSCRIPTION

Cells transcribe four main types of RNA from DNA

RNA primer molecules for DNA polymerase to use during DNA
replication

messenger RNA (mRNA) molecules, which carry genetic information
from chromosomes to ribosomes

ribosomal RNA (rRNA) molecules, which combine with ribosomal
polypeptides to form ribosomes-the organelles that synthesize
polypeptides

transfer RNA (tRNA) molecules, which deliver amino acids to the
ribosomes
Initiation of Transcription

RNA polymerases - the enzymes that
synthesize RNA bind to specific nucleotide
sequences called promoters, each of
which is located near the beginning of a
gene and initiates transcription.
Initiation of Transcription

In bacteria, a polypeptide subunit of RNA polymerase called the
sigma factor is necessary for recognition of a promoter.

Once it adheres to a promoter sequence, RNA polymerase unwinds
and unzips the DNA molecule in the promoter region and then
travels along the DNA, unzipping the double helix as it moves.

One type of RNA polymerase transcribes RNA primer, and a second
type of RNA polymerase transcribes mRNA, rRNA, and tRNA.

A cell uses different sigma factors and different promoter sequences
to provide some control over the relative amount of transcription.
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RNA polymerases with different sigma factors do not adhere equally
strongly to all promoters; there is about a 100-fold difference
between the strongest attraction and weakest one. The greater the
attraction between a particular sigma factor and a promoter, the
more likely that transcription will proceed. Ultimately, variations in
sigma factors and promoters affect the amounts and kinds of
polypeptides produced.
Elongation of the RNA Transcript
Elongation of the RNA Transcript

Like DNA polymerase, RNA polymerase links nucleotides in the 5' to
3' direction only; however, RNA polymerase differs from DNA
polymerase in the following ways:

RNA polymerase unwinds and opens DNA by itself; helicase is not
required.
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RNA polymerase does not need a primer.
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RNA polymerase is slower than DNA polymerase, proceeding at a
rate of about 50 nucleotides per second.
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RNA polymerase incorporates ribonucleotides instead of
deoxyribonucleotides.
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Uracil nucleotides are incorporated instead of thymine nucleotides.
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The proofreading function of RNA polymerase is less efficient,
leaving a base pair error about every 10,000 nucleotides.
Termination of Transcription
Termination of Transcription:
Self-Termination

Self-termination occurs when RNA polymerase transcribes a terminator sequence of
DNA composed of two symmetrical series:

one that is very rich in guanine and cytosine bases, followed by a region rich in
adenine bases.

RNA polymerase slows down during transcription of the GC rich portion of the
terminator because the three hydrogen bonds between each guanine and cytosine
base pair make unwinding the DNA helix more difficult.

This pause in transcription, which lasts about 60 seconds, provides enough time for
the RNA molecule to form hydrogen bonds between its own symmetrical sequences,
forming a stem and loop structure that puts tension on the union of RNA polymerase
and the DNA.

When RNA polymerase transcribes the adenine-rich portion of the terminator, the
relatively few hydrogen bonds between the adenine bases of DNA and the uracil
bases of RNA cannot withstand the tension, and the RNA transcript breaks away from
the DNA, releasing RNA polymerase.
Termination of Transcription:
Rho-Dependent Termination

The second type of termination depends on a
termination protein, called Rho, that binds to a
specific RNA sequence near the end of an RNA
transcript.

The protein moves toward the 3' end, pushing
between RNA polymerase and the DNA strand
and forcing them apart; this releases RNA
polymerase and the RNA transcript.
TRANSLATION

Translation is the process whereby
ribosomes use the genetic information of
nucleotide sequences to synthesize
polypeptides composed of specific amino
acid sequences.

How do ribosomes interpret the nucleotide
sequence of mRNA to determine the
correct order in which to assemble amino
acids?
The Genetic Code

Genes are composed of sequences of
three nucleotides that specify amino acids.
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For example, the DNA nucleotide sequence
TTT specifies the amino acid lysine, and
TTA codes for asparagine.
5’ end
U
C
Middle base
U
C
A
phe ser tyr
phe ser tyr
leu ser end
leu ser end
leu pro his
leu pro his
leu pro gln
leu pro gln
3’ end
G
cys
cys
end
trp
arg
arg
arg
arg
U
C
A
G
U
C
A
G
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Code Quiz
Click for the answer.
1. CCU codes for: ?
2. CGA codes for: ?
3. UCA codes for: ?
1. pro
2. arg
5’
U
C
3. ser
A
U
C
A
G
Phe
Ser
Tyr
Cys
Phe
Ser
Tyr
Cys
Leu
Ser
End
End
Leu
Ser
End
Trp
Leu
Pro
His
Arg
Leu
Pro
His
Arg
Leu
Pro
Gln
Arg
Leu
Pro
Gln
Arg
Ile
Thr
Asn
Ser
3’
U
C
A
G
U
C
A
G
U
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64 possible arrangements - more than enough to
specify 21 amino acids.
the genetic code define as triplets of mRNA
nucleotides called codons that code for specific
amino acids.
61 codons specify amino acids and 3 codons
-UAA, UAG, and UGA-to stop translating
UGA codes for the 21st amino acid,
selenocysteine.
Codon AUG also has a dual function, acting as
both a start signal and coding for an amino acid –
methionine.
Some exceptions of the genetic code
Codon
Usual use
Alternative use
AUA
Codes for isoleucine
Codes for methionine in mitochondria
UAG
STOP
Codes for glutamine in some protozoa
and algae and for pyrrolysine (22nd amino
acid) in some prokaryotes
CGG
Codes for arginine
Codes for tryptophan in plant
mitochondria
UGA
STOP, selenocysteine
Codes for tryptophan in mitochondria and
mycoplasmas (type of bacteria)
Participants in Translation:
Messenger RNA

Messenger RNA carries genetic information (in the form of RNA nucleotide
sequences) from a chromosome to ribosomes.

In prokaryotes a basic mRNA molecule contains sequences of nucleotides
that are recognized by ribosomes:
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an AUG start codon, sequential codons for other amino acids in the
polypeptide, and at least one of the three stop codons. A single molecule of
prokaryotic mRNA often contains a start codon and instructions for more
than one polypeptide arranged in series.

Because both transcription and the subsequent events of translation occur
in the cytosol of prokaryotes, prokaryotic ribosomes can begin translation
before transcription is finished.
Participants in Translation:
Transfer RNA
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tRNA molecule is a
sequence of about 75
ribonucleotides that curves
back on itself to form three
main hairpin loops (a)
For simplicity, tRNA will be
represented in subsequent
figures by an icon shaped
like the illustration (b)
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A molecule of tRNA transfers the correct amino acid to a
ribosome during polypeptide synthesis. To this end, tRNA has
an acceptor stem for a specific amino acid at its 3' end, and
an anticodon triplet in its bottom loop.

The existence of only one specific charging enzyme for each
amino acid ensures that every tRNA molecule carries only
one specific amino acid.
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Anticodons are complementary to mRNA codons, and each
acceptor stem is designed to carry one particular amino acid,
which varies with the tRNA.
Participants in Translation:
Ribosomes and ribosomal RNA
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Prokaryotic ribosomes, which are also called 70S ribosomes based
on their sedimentation rate in an ultracentrifuge, are extremely
complex associations of ribosomal RNAs and polypeptides. Each
ribosome is composed of two subunits: 50S and 30S.

The 50S subunit is in turn composed of two rRNA molecules (23S
and 5S) and about 34 different polypeptides, whereas the 30S
subunit consists of one molecule of 165 rRNA and 21 ribosomal
polypeptides. The ribosomes of mitochondria and chloroplasts are
also 70S ribosomes composed of the similar subunits and
polypeptides.
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In contrast, both the cytosol and the rough endoplasmic reticulum
(RER) of eukaryotic cells have 80S ribosomes composed of 60S
and 40S subunits. These subunits contain larger molecules of rRNA
and more polypeptides than the corresponding prokaryotic
subunits, though researchers do not agree on the exact number of
polypeptides. The term eukaryotic ribosome is understood to mean
only the 80S ribosomes of the cytosol and RER. Since the
ribosomes of mitochondria and chloroplasts are 70S, they are
called prokaryotic ribosomes even though they are in eukaryotic
cells.
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Each ribosome also has three tRNA binding sites
that are named for their function:
1) The A site accommodates a tRNA
delivering an amino acid.
2) The P site holds a tRNA and the growing
polypeptide.
3) Discharged tRNAs exit from the E site.
Stages of Translation
Initiation: the events
1) The smaller ribosomal
subunit attaches to
mRNA at a ribosome
binding site (also
known as a ShineDalganno sequence
after its discoverers),
with a start codon at its
P site.
2) tRNA £Met (whose
anticodon is
complementary to
the start codon)
attaches at the
ribosome's P site;
GTP supplies the
energy required for
binding.
3) The larger
ribosomal subunit
attaches to form
a complete
initiation complex.
Stages of Translation
Elongation
1) The transfer RNA whose
anticodon matches the next
codon - in this case,
phenylalanine (Phe) - delivers
its amino acid to the A site.
Another protein called
elongation factor escorts the
tRNA along with a molecule of
GTP. Energy from GTP is
used to stabilize each tRNA
as it is added to the A site.
2) A ribozyme in the larger
ribosomal subunit forms a
peptide bond by dehydration
synthesis between the terminal
amino acid of the growing
polypeptide chain (in this case,
N-formylmethionine) and the
newly introduced amino acid.
The polypeptide is now
attached to the tRNA
occupying the A site.
3) Using energy supplied by more
GTP, the ribosome moves one
codon down the mRNA. This
transfers each tRNA to the
adjacent binding site; that is,
the first tRNA moves from the
P site to the E site, and the
second tRNA (with the
attached polypeptide) moves
to vacated P site.
4) The ribosome releases
the “empty" tRNA from
the E site. In the cytosol,
the appropriate enzyme
recharges it with
another molecule of its
specific amino acid.
5) The cycle repeats, each
time adding another
amino acid (in this case,
threonine, then alanine,
and then glutamine).
Stages of Translation
Termination

Termination does not involve tRNA; instead, proteins called
release factors halt elongation.

It appears that release factors somehow recognize stop
codons and modify the larger ribosomal subunit in such a
way as to activate another of its ribozymes, which severs the
polypeptide from the final tRNA (resident at the P site). The
ribosome then dissociates into its subunits.
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Termination of translation should not be confused with
termination of transcription. The polypeptides released at
termination may function alone as proteins, or they may
function together in quarternary protein structures.
Regulation of Genetic
Expression
About 75% of genes are expressed at all times; that is, they are
constantly transcribed and translated and play a persistent role in
the phenotype.
These genes code for RNAs and polypeptides that are needed in
large amounts by the cell for example, integral proteins of the
cytoplasmic membrane, structural proteins of ribosomes, and
enzymes of glycolysis.
Other genes are regulated so that the polypeptides they encode are
synthesized only when a cell has need of them. Protein synthesis
requires a large amount of energy, which can be conserved if a cell
forgoes production of unneeded polypeptides.
Cells regulate protein synthesis in many ways. They may stop
translation directly or stop polypeptide synthesis by stopping mRNA
transcription.
Control of Translation
Some regulation of genetic expression is at the level of
translation; that is, cells control which mRNA molecules
are translated into polypeptides.
One way a cell establishes control involves so-called
riboswitches. A riboswitch is a molecule of mRNA that
changes its shape in response to an alteration in
temperature or a shift in the concentration of a nutrient,
such as a vitamin, nucleotide base, or amino acid.
Riboswitches fold in such a way as to block ribosomes
and translation of the polypeptide they encode when that
polypeptide is not needed by the cell.
Another method of translational control
involves short interference RNA (siRNA),
which is an RNA molecule complementary
to a portion of mRNA, tRNA, or a gene.
Such RNA molecules are also called
antisense RNA. siRNA binds to its
complementary nucleic acid, rendering its
target inactive.
OPERON
An operon consists of a promoter and a series of genes, which code for
enzymes and structures such as channel proteins.
Some operons are controlled by an adjacent regulatory element called an
operator where a repressor protein binds to stop transcription.
Such operons are either repressed (turned off) or induced (turned on) by
proteins coded by a regulatory gene (located elsewhere).
Inducible operons are not usually transcribed and must be activated by
inducers.
Repressible operons operate in reverse fashion-they are transcribed
continually until deactivated by repressors.
The Lactose Operon, an Inducible Operon
The lactose (lac) operon is inducible operon. It includes a
promoter, an operator, and three genes that encode for
protein involved in the catabolism of lactose.
The operon is controlled by a regulatory gene that is
constantly transcribed and translated to produce a
repressor protein that attaches to DNA at the lac operator.
This repressor prevents RNA polymerase from moving beyond the promoter, stopping synthesis of mRNA. Thus, the
lac operon is usually inactive.
Whenever lactose becomes available, the cell takes in lactose and converts
it to allolactose - an inducer that changes the quaternary structure of the
repressor so that it is inactivated and can no longer attach to DNA.
This absence of binding allows transcription of the three structural genes to
proceedthe operon has been induced and has become active. Ribosomes
translate the newly synthesized mRNA to produce enzymes that catabolize
lactose.
Once the lactose supply has been depleted, there is no more inducer, and
the repressor once again becomes active, suppressing transcription and
translation of the lac operon. In this manner, its conserve energy by
synthesizing enzymes for the catabolism of lactose only when lactose is
available to them.
Such inducible operons are often involved in controlling catabolic pathways
whose polypeptides are not needed
The Tryptophan Operon, a
Repressible Operon
The tryptophan (trp) operon, which consists of a promoter, an
operator, and five genes that code for the enzymes involved in the
synthesis of tryptophan, is an example of such a repressible operon.
Just as with the lac operon a regulatory gene codes for a repressor
molecule that is constantly synthesized. In contrast to inducible
operons however, the repressor of repressible operons is normally
inactive.
In the case of the repressible trp operon whenever tryptophan is not
present in the environment, the trp operon inactive:
The appropriate mRNA is transcribed the enzymes for tryptophan
synthesis are translated, and tryptophan is produced (Figure a).
When tryptophan is available, it activates the repressor by binding to
it. The activated repressor then binds to the operator, halting the
movement of RNA polymerase and halting transcription (Figure b).
In other words, tryptophan acts as a corepressor of its own
synthesis.
The roles of operons in the
regulation of transcription
Type of
regulation
Type of metabolic
pathway regulated
Regulating
condition
Inducible
operons
Catabolic pathways Presence of
substrate of
pathway
Repressible Anabolic pathways Presence of
operons
product of
pathway
Mutations of Genes:
Types of mutation
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Mutations range from large changes in an
organism's genome, such as the loss or gain of an
entire chromosome, to the most common type of
mutation - point mutations - in which just one
nucleotide base pair is affected.
Mutations include base pair insertions,
deletions, and substitutions.
Substitution of a nucleotide of similar shape - a
purine for a purine or pyrimidine for a pyrimidineis called a transition.
Substitution of a purine for a pyrimidine or vice
versa is called a transversion.
The following analogy illustrates some types of mutations.
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Suppose that the DNA code was represented by the letters
THECATATEELK.
Grouping the letters into triplets (like codons) yields
THE CAT ATE ELK.
The substitution of a single letter could either change the meaning of the sentence,
as in THE RAT ATE ELK, or result in a meaningless phrase, such as THE CAT RTE ELK.
Insertion or deletion of a letter produces more serious changes, such as
TRH ECA TAT EEL K or TEC ATA TEE LK.
Insertions and deletions are also called frame shift mutations because nucleotide
triplets subsequent to the mutation are displaced, creating new sequences of
codons that result in vastly altered polypeptide sequences.
Frameshift mutations affect proteins much more seriously than mere substitutions
because a frame shift affects all co dons subsequent to the mutation.
Mutations can also involve inversion (THE ACT ATE KLE),
duplication (THE CAT CAT ATE ELK ELK), or
transposition (THE ELK ATE CAT).
Such mutations and even larger deletions and insertions are gross mutations.
Effects of Mutations
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Some base-pair substitutions
produce silent mutations
because the substitution does
not change the amino acid
sequence because of the
redundancy of the genetic code.
For example, when the DNA
triplet AAA " is changed to AAG,
the mRNA codon will be
changed from UUU to UUC;
however, because both codons
specify the amino acid
phenylalanine, there is no
change in the phenotype - the
mutation is silent because it
affects the genotype only.
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Of greater concern are substitutions that
change a codon for one amino acid into a
codon for a different amino acid.
A change in a nucleotide sequence resulting
in a codon that specifies a different amino
acid is called a missense mutation; what
gets transcribed and translated makes
sense, but not the right sense.
The effect of missense mutations depends
on where in the protein the different amino
acid occurs.
When the different amino is in a critical
region of a protein, the protein becomes
nonfunctional; however, when the different
amino acid is in a less important region, the
mutation has no adverse effect.
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A third type of mutation
occurs when a base-pair
substitution changes an
amino acid codon into a
stop codon.
This is called a nonsense
mutation. Nearly all
nonsense mutations
result in nonfunctional
proteins.

Frameshift mutations
(that is, insertions or
deletions) typically
result in drastic
missense and
nonsense mutations,
except when the
insertion or deletion
is very close to the
end of a gene
Mutagens
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Mutations occur naturally during the life of an organism.
Such spontaneous mutations result from errors in
replication and repair as well as from recombination in
which relatively long stretches of DNA move among
chromosomes, plasmids, and viruses, introducing frame
shift mutations.
Further, though cells have repair mechanisms to reduce
the effect of mutations, the repair process itself can
introduce additional errors.
Physical or chemical agents called mutagens, which
include radiation and several types of DNA-altering
chemicals, induce mutations.
Radiation
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Ioning radiation, such as X rays and gamma rays, can cause some
of the molecules within cells to lose electrons, becoming highly
reactive ions and free radicals.
Some of these reactive ions and free radicals can combine with
bases on DNA, resulting in errors in DNA replication and therefore
mutations. Even more seriously, these groups can react with the
sugar-phosphate backbone of DNA, causing breaks in chromosomes.
Nonionizing radiation in the form of UV light is also mutagenic
because it can cause adjacent thymine bases to covalently bind to
another, producing thymine dimmers.
Such dimmers can cause serious harm or death to a cell if they are
not repaired, since these dimmers prevent the cell from properly
transcribing or replicating such DNA.
Chemical Mutagens :
Nucleotide Analogs
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nucleotide analogs are compounds that
are structurally similar to normal
nitrogenous bases, but with different
base-pairing properties.
These compounds can become
incorporated into growing DNA during
replication, replacing their related base.
Once incorporated, the nucleoside
analog can inhibit further replication, or
cause mismatching in a future round of
replication.
For example, 5-bromouracil is a
nucleoside analog of thymine, but it
often pairs with guanine rather than
adenine. Incorporation of 5-bromouracil
can therefore lead to a base substitution
mutation of a guanine for an adenine.
Chemical Mutagens :
Nucleotide-Altering Chemicals

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some chemical mutagens directly alter the
structures of the nitrogenous bases of
DNA.
For example, nitrous acid can chemically
alter adenine bases so that they base pair
with cytosine, rather than thymine.
During replication, this change causes
base substitution mutations in the
daughter DNA.
Chemical Mutagens :
Frameshift Mutagens


some chemical
mutagens cause small
insertions or
deletions of
nucleotide base pairs,
which can lead to
frameshift mutations.
Examples of such
frameshift mutagens
include acridine, a
dye commonly used
as a mutagen in
genetic research
Frequency of Mutation

Mutations are rare events.

Organisms could not live or effectively reproduce themselves. About
one of every ten million (107) genes contains an error.

Mutagens typically increase the mutation rate by a factor of 10-1000
times; mutagens induce an error in one of every 104 to 106 genes.

Most mutations are deleterious because they code for nonfunctional
proteins or stop transcription entirely. Cells, without functional
proteins cannot metabolize; any deleterious mutations are removed
from the population when the cells die.

Rarely, a cell acquires a beneficial mutation that allows it to survive,
reproduce, and pass the mutation to its descendants.

For example, a bacterium night randomly acquire a mutation that
confers resistance to an antibiotic.
DNA Repair

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Although a mutation might rarely convey
an advantage, most mutations are
deleterious.
Methods for repairing damaged DNA,
including light and dark repair of
pyrimidine dimers, base-excision repair,
mismatch repair, and an S0S response.
Repair of Pyrimidine Dimers

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Many cells contain DNA photolyase, an enzyme that is activated by
visible light to break the bonds between adjoining pyrimidine
nucleotides, reversing the mutation and restoring the original DNA
sequence.
Light repair mechanism is advantageous for the prokaryote, but it
presents a difficulty to scientists studying UV-induced mutations-they must keep such strains in the dark, or the mutants revert to
their previous form.
Dark repair involves a different repair enzyme-one that doesn't
require light. Dark repair enzymes cut the damaged section of DNA
from the molecule, creating a gap that is repaired by DNA
polymerase I and DNA ligase. Dark repair operates either in light or
in the dark.
Base-Excision Repair


Sometimes DNA polymerase III incorporates an
incorrect nucleotide during DNA replication. If
the proofreading function of DNA polymerase III
does not repair the error, cells may use another
enzyme system in a process called base-excision
repair.
This enzyme system excises the erroneous base,
and then DNA polymerase I fills in the gap
Mismatch Repair

A similar repair mechanism is called mismatch repair.

Mismatch repair enzymes scan newly synthesized DNA looking for
mismatched bases, which they remove and replace.

How does the mismatch repair system determine which strand to
repair? If it chose randomly, 50% of the time it would choose the
wrong strand and introduce mutations.

Mismatch repair enzymes, however, do not choose randomly.

They distinguish between a new DNA strand and an old strand
because old strands are methylated.
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Recognition of an error as far as 1000 base pairs away from an
unmethylated portion of DNA triggers the mismatch repair enzymes.
Once a new DNA strand is methylated, mismatch repair enzymes
cannot correct any errors that remain.
SOS Response
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Sometimes damage to DNA is so extreme that regular
repair mechanisms cannot cope with the damage.
In such cases, bacteria resort to what geneticists call an
S0S response involving a variety of processes, such as
the production of novel DNA polymerases (IV and V)
capable of copying less-than-perfect DNA.
These polymerases replicate DNA with little regard to the
base sequence of the template strand.
Of course, this introduces many new and potentially fatal
mutations, but presumably SOS repair allows a few
offspring of these bacteria to survive.