A nonsense mutation is a point mutation that introduces a premature stop codon into the coding region of a gene. This results in only a partial protein being produced, as the stop codon signals the ribosome to terminate translation early. These truncated proteins are often nonfunctional or defective. The lac operon regulates genes involved in lactose metabolism in E. coli. It is negatively regulated by the lac repressor protein, which binds to the operator region and blocks transcription when lactose is absent. However, in the presence of lactose or another inducer molecule, the repressor dissociates from the DNA, allowing transcription and expression of the genes required to break down and utilize lactose. Gene regulation in prokary

1. 1
Mutation
Gene mutation

2. 2
◘ Point Mutations:
 Point mutations are changes in one base pair of a cell's DNA sequence.
 For example, if an A in the DNA code is changed to a C, that is a point
mutation.
 Point mutations in the coding region of a gene can have different effects
depending on the resulting changes to the codons in the messenger
RNA.
 There are a few major kinds of point mutations: missense mutations,
nonsense mutations, silent mutations and read through mutations.
 Here, we're going to focus on nonsense mutations, which are mutations
that introduce a premature stop codon into the coding sequence of a
gene.
◘ Nonsense Mutation Definition
 When you think about a mutant, you might think about sci-fi movies
where mutated creatures become powerful and evil and then attempt to
destroy the world.
 But what are mutations, really?
 Mutations are changes to a cell's DNA sequence, and there are several
different types.
 A nonsense mutation is a point mutation that introduces a premature
stop codon into the part of the gene that encodes a protein.

3. 3
 A stop codon is like a period at the
end of a sentence.
 It instructs the ribosome to stop
making the protein.
 So, if a mutation leads to an early
stop codon, only part of the protein
will be made.
 Half-baked proteins that result from
nonsense mutations are often nonfunctional or defective.
 Now let's learn more about how nonsense mutations work and their
consequences.
Gene vs. Chromosomal Mutations
Gene Mutations Chromosomal Mutations
• Mistakes that affect individual
genes on a chromosome.
• One base substitutes for
another on a DNA strand and
leads to the wrong protein
being made; this affects one or
more functions within the
organism.
• Mistakes that affect the whole
chromosome.
• There are four types of
chromosomal mutations:
duplication, deletion,
inversion, and translocation.
• ALL MUTATIONS ARE
CAUSED BY MUTAGENS.
♣ A chromosome abnormality, disorder, anomaly, aberration,
or mutation is a missing, extra, or irregular portion of chromosomal DNA.

4. 4

5. 5

6. 6
◘ Aberration:
 Whether chromosome aberrations (after the mitosis) are induced by
single-strand breaks or double-strand breaks in the structure determines
the fate of the cell.
 In single-strand breaks, the chromosome tends to repair by joining the
two fragments in a process called restitution, provided sufficient time is
allowed.
 The cell becomes functionally normal and replicates normally.
 However, if the fragments are replicated during DNA synthesis prior to
restitution, two strands with centromeres and two strands without
centromeres will be produced.
 Random combination of these fragments will then produce acentric and
dicentric chromatids.
 Such chromosomes suffer severe consequences due to the mismatch of
genetic information.

7. 7
 In another scenario, radiation
can cause two breaks in one arm
of a chromosome, resulting in
three fragments:
 Only two of which combine with
the loss of the third.
 Such a process is called deletion.
 Combination of all three fragments
into a chromosome with changes
along the broken line.
 This process is called inversion,
◘ If radiation produces single-strand break in two separate
chromosomes, then there are four ways of recombining the broken ends:
A. The dicentric and acentric combinations are similar to those formed
after replication of single strands in the same chromosome.
B. Translocation is a process in which
two fragments
• One with a centromere from one
chromosome and one without a
centromere from another chromosome
combine to form a new chromosome.

8. 8
◘ Philadelphia chromosome or Philadelphia translocation
• Is a specific chromosomal abnormality that is associated with
chronic myelogenous leukemia (CML).
• It is the result of a reciprocal translocation between chromosome
9 and 22, and is specifically designated t(9;22)(q34;q11).
• The presence of this translocation is a highly sensitive test for
CML, since 95% of people with CML have this abnormality.

9. 9
• However, the presence of the
Philadelphia (Ph) chromosome is
not sufficiently specific to
diagnose CML, since it is also
found in acute lymphoblastic
leukemia and occasionally in acute
myelogenous leukemia (AML).
• The result of the translocation is the oncogenic BCR-ABL gene fusion,
located on the shorter derivative 22 chromosome.
• This translocation is designated t (9;22).
• It results in one chromosome 9 longer than normal and one
chromosome 22 shorter than normal.
• The latter is called the Philadelphia chromosome and designated Ph1
.
• The DNA removed from chromosome 9 contains most of the proto-
oncogene designated c-ABL.
• The break in chromosome 22 occurs in the middle of a gene designated
BCR.
• The resulting Philadelphia chromosome has the 5' section of BCR fused
with most of c-ABL.
Genetic make up

10. 10
◘ Genes playing role in cancer development:
• Oncogenes.
• Tumor suppressor genes.
• DNA repair genes.
◘ Viruses and Cancer
Those are directly oncogenic, infecting and persisting in the
cancer cells, e.g. most DNA tumor viruses.
Those that act indirectly, promoting conditions that allow tumor
cells to progress to cancer,
• e.g. hepatitis C virus and Human Immunodeficiency Virus
(HIV).

11. 11
♣ Retroviruses:
• Comprise a group of related viruses in which the viral genetic
information is converted from RNA to a DNA form during infection
of animal cells.
• In its DNA form the viral information inserted into the host
chromosomes.
• From a chromosomal position, the viral DNA
directs the synthesis of viral RNA and proteins,
which then spontaneously assemble to form
progeny virus.
• Viruses of this type have been detected in many
animal species, and some have been popularly
called RNA tumor viruses because of their
association with tumors and leukemias.
♠ Retroviruses are thought to cause tumors in two general ways:
♣ First, viral integration can occur near or within an important
control gene in the host chromosome, raising the level of
expression of that gene in a way that leads to uncontrolled
cellular growth.
• In general, the probability of this happening is low because
viral integration is not specifically targeted for these sites.

12. 12
♣ Second, the virus itself may carry a gene whose product
disrupts normal cellular control pathways.
• These virally borne ‘control genes’ are called oncogene, and
they tend to produce tumor cells at a high frequency.
• Viral oncogenes are often defective copies of cellular regulatory
genes.
• Oncogenic viruses cause cancer by inducing changes that affect cell
growth and division
• Oncogenes frequently interfere with the normal functioning of the
viral genes responsible for producing new virus.
• Thus tumor viruses are often defective and sometimes require
‘helper’ viruses to reproduce.
• One important class of oncogene is called ras genes are a small
family of related genes found normally in a variety of eukaryotic
organisms ranging from yeast to humans.
• They are associated with a variety of human and rodent tumors, and
genes ras have been found as oncogenes in mouse and rat
retroviruses.
• Nucleotide sequence comparison between normal ras genes and
oncogenic ones in retroviruses indicate that oncogenic ras genes
contain mutations.
• Thus it may be that some carcinogens cause cancer by chemically
modifying the ras region of the DNA.
• Normal ras genes can also produce malignancy if the ras proteins are
produced in very large amounts.

13. 13
• This can occur if a very strong promoter is placed immediately
upstream from the genes.
• Cell transformation: the ability of viruses to alter cell in culture has
been critical to identifying oncogenes.
Control Of Gene expression
◘ Operons
• Operons are groups of genes that function to produce proteins
needed by the cell.
♦ There are two different kinds of genes in operons:
1- Structural genes code for proteins needed for the normal operation of the
cell.
- For example, they may be proteins needed for the breakdown of sugars.
- The structural genes are grouped together and a single mRNA molecule is
produced during their transcription.
2- Regulator genes code for proteins that regulate other genes.

14. 14
• An operon is a functioning unit of key nucleotide sequences
including an operator, a common promoter, and one or more
structural genes, which is controlled as a unit to produce
messenger RNA (mRNA), in the process of protein
transcription.
• Operons have not been found in eukaryotes
◘ The Operon as a unit of transcription
• An operon contains one or more structural genes which are
transcribed into one polycistronic mRNA: a single mRNA
molecule that codes for more than one protein.
• Upstream of the structural genes lies a promoter sequence which
provides a site for RNA polymerase to bind and initiate
transcription.
• Close to the promoter lies a section of DNA called an operator.
• The operon may also contain regulatory genes such as a
repressor gene which codes for a regulatory protein that binds to
the operator and inhibits transcription.
• Regulatory genes need not be part of the operon itself, but may
be located elsewhere in the genome.
• The repressor molecule will reach the operator to block the
transcription of the structural genes.

15. 15
• In bacteria, control of the rate of transcriptional initiation is the
predominant site for control of gene expression.
• As with the majority of prokaryotic genes, initiation is controlled
by two DNA sequence elements that are approximately 35 bases
and 10 bases, respectively, upstream of the site of transcriptional
initiation and as such are identified as the -35 and -10 positions.

16. 16
• These 2 sequence elements are termed promoter sequences,
because they promote recognition of transcriptional start sites
by RNA polymerase.
• The consensus sequence for the -35 position is TTGACA, and
for the -10 position, TATAAT.
• (The -10 position is also known as the Pribnow-box.)
• These promoter sequences are recognized and contacted by
RNA polymerase.
Promoter

17. 17
Prokaryotic Promoter
♦ The lac operon
 Glucose Absent, Lactose Present: Transcription of the lac
operon.
• The lac operon of the model bacterium Escherichia coli was the
first operon to be discovered and provides a typical example of
operon function.
• It consists of three adjacent structural genes, a promoter, a
terminator, and an operator.

18. 18
• The lac operon is regulated by several factors including the
availability of glucose and lactose.
• For E. coli, glucose is the preferred sugar.
• When glucose is present, there is no need to use lactose: these
genes are not transcribed.
• When there is no glucose, E. coli has to use other sugars.
• IF lactose is present, the genes for lactose utilization will be
made.
• Conversely, if there is no lactose, they genes remain locked
down.
 Glucose Present: No transcription
 Glucose Absent: Minimal transcription

19. 19
♦There are two modes of regulation of the initiation of transcription in
operons:
 Positive control mode
- Where the interaction between the regulatory protein and regulatory
region on the DNA turn the transcription on.
- The genes are off by default and are turned on by the activators.
- Transcription factors interact with the RNA polymerase and assist the
enzyme in initiating transcription at the promoter.
- This positive fashion of controlling gene expression is more common in
eukaryotes than in prokaryotes.
 Negative control mode:
- Where the interaction turns the genes off.
- In this case, a repressor protein binds the operator, a DNA sequence
of approximately 20 to 25 nucleotides, which is next to the promoter or
juxtaposed, and prevents the RNA polymerase from initiating
transcription.
- To switch on the system, small molecules called inducers trigger the
production of proteins by binding to the repressor protein and changing
its conformation.
- This change alters the operator-repressor interaction, so that the
repressor can no longer remain attached to the operator.
- Negative control is widely used among prokaryotes, which need to
respond swiftly to changes in the environment.

20. 20
 Regulation in Prokaryotes
- Bacteria have a simple general mechanism for coordinating the
regulation of genes that encode products involved in a set of
related processes.
- The gene cluster and promoter, plus additional sequences that
function together in regulation are called an operon.
 The Lactose Operon (lac operon)
- The lactose operon of E. coli encodes the enzyme b-
galactosidase which hydrolyzes lactose into galactose and
glucose.

21. 21
Lac operon
• The Z gene encodes for b-galactosidase.
• The Y gene encodes a permease that facilitates the transport of
lactose into the bacterium.
• The A gene encodes a thiogalactoside transacetylase whose
function is not known.
• All three of these genes are transcribed as a single, polycistronic
mRNA.
• Polycistronic RNA contains multiple genetic messages each with
its own translational initiation and termination signals.
♦ Negative Control of the lac Operon
• The protein that inhibits transcription of the lac operon is a
tetramer with four identical subunits called lac repressor.
• The lac repressor is encoded by the lacI gene, located upstream
of the lac operon and has its own promoter.
• Expression of the lacI gene is not regulated and very low levels
of the lac repressor are continuously synthesized.
• Genes whose expression is not regulated are called constitutive
genes.

22. 22
• In the absence of lactose the lac repressor blocks the expression of the
lac operon by binding to the DNA at a site, called the operator that is
downstream of the promoter and upstream of the transcriptional
initiation site.
• The operator consists of a specific nucleotide sequence that is
recognized by the repressor which binds very tightly, physically
blocking (strangling) the initiation of transcription.
• The lac repressor has a high affinity for lactose.
• When a small amount of lactose is present the lac repressor will bind it
causing dissociation from the DNA operator thus freeing the operon for
gene expression.
• Substrates that cause repressors to dissociate from their operators are
called inducers and the genes that are regulated by such repressors are
called inducible genes.

23. 23
Lac Operon

24. 24
Negative regulation by repressor
•‫ال‬diagrams‫للتوضيح‬ ‫كدا‬ ‫غير‬ ‫علينا‬ ‫اللي‬ ‫هي‬ ‫اسود‬ ‫بإطار‬ ‫اللي‬♥