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To know and explain:• Regulation of Bacterial Gene Expression

• Constitutive ( house keeping) vs. Controllable genes

• OPERON structure and its role in gene regulation

• Regulation of Eukaryotic Gene Expression at different levels:

• DNA methylation

• Histon modifications(Chromatin Remodeling)

• Increasing the number of gene copies (gene amplification)

• Changing the rate of initiation of transcription

• Alternate splicing

• mRNA stability

• Changing the rate of initiation of translation

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Gene expression is the process by which the information

encoded in a gene is used to direct the assembly of a protein

molecule.

Gene expression is explored through a study of protein structure

and function, transcription and translation, differentiation and

stem cells.

It is the process by which information from a gene is used in the

synthesis of a functional gene product.

These products are often proteins, but in non-protein coding

genes such as ribosomal RNA (rRNA), transfer RNA (tRNA) or

small nuclear RNA (snRNA) genes, the product is a functional

RNA.

The process of gene expression is used by all known life -

eukaryotes (including multicellular organisms), prokaryotes

(bacteria and archaea)

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• Regulation of gene expression includes a wide range of

mechanisms that are used by cells to increase or decrease

the production of specific gene products (protein or RNA).

• Gene regulation is essential for viruses, prokaryotes and

eukaryotes as it increases the versatility and adaptability of

an organism by allowing the cell to express protein when

needed.

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• Although a functional gene product may be an RNA or a

protein, the majority of known mechanisms regulate protein

coding genes.

• Any step of the gene's expression may be modulated, from

DNA-RNA transcription to the post-translational modification

of a protein.

• The first discovered example of a gene regulation system was

the lac operon, discovered by Jacques Monod, in which

protein involved in lactose metabolism are expressed by

E.coli only in the presence of lactose and absence of glucose.

• Gene regulation drives the processes of cellular

differentiation and morphogenesis, leading to the creation of

different cell types in multicellular organisms where the

different types of cells may possess different gene expression

profile.

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Genes are subunits of DNA, the information

database of a cell that is contained inside the cell

nucleus.

This DNA carries the genetic blueprint that is used to

make all the proteins the cell needs.

Every gene contains a particular set of instructions

that code for a specific protein

Constitutive ( house keeping) genes:

Are expressed at a fixed rate, irrespective to the cell

condition.

Their structure is simpler.

Controllable genes:Are expressed only as needed. Their amount may

increase or decrease with respect to their basal level in different condition.

Their structure is relatively complicated with some response elements

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When the expression of genetic information is quantitatively

increased by the presence of specific regulatory element is

known as positive regulation.

Element modulating positive regulation is known as activator or

positive regulator.

When the expression of genetic information is diminished by

the presence of specific regulatory element is known as

negative regulation.

The element or molecule mediating the negative regulation is

said to be repressor.

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Type A response:

Type B response:

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1) RNA polymerase binds to DNA at promoters.

2)Transcription initiation is regulated by proteins

that bind to or near promoters.

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Synthesis of the primary RNA transcript (transcription)

Posttranscriptional modification of mRNA

Messenger RNA degradation

Protein synthesis ( translation )

Posttranslational modification of proteins

Protein targeting & transport

Protein degradation10/25/2014 14

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In prokaryotes the primary control point is the process of

transcription initiation .

Different ways for regulation of gene expression in bacteria:

Regulation of gene expression can be done by some operon

pathways such as

1.lac operon.

2.tryptophan operon.

.

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Transcriptional control

Translational control

Post translational control

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In genetics, an operon is a functioning unit of genomic DNA

containing a cluster of genes under the control of a single

promoter.

Operons occur primarily in prokaryotes but also in some

eukaryotes.

Operons are related to regulons, stimulons and modulons.

An operon is made up of several structural genes arranged

under a common promoter and regulated by a common

operator.

It is defined as a set of adjacent structural genes, plus the

adjacent regulatory signals that affect transcription of the

structural genes.

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An operon is made up of 4 basic DNA components:

Promoter – a nucleotide sequence that enables a gene to be

transcribed. The promoter is recognized by RNA polymerase, which then

initiates transcription.

Regulator – These genes control the operator gene in cooperation

with certain compounds called inducers and corepressors present in the

cytoplasm.

Operator – a segment of DNA that a repressor binds to. It is

classically defined in the lac operon as a segment between the

promoter and the genes of the operon.

Structural genes – the genes that are co-regulated by the

operon.

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Operon regulation can be either negative or positive by induction or

repression.

Negative control involves the binding of a repressor to the

operator to prevent transcription.

In negative inducible operons, a regulatory repressor protein is normally

bound to the operator, which prevents the transcription of the genes on

the operon .

If an inducer molecule is present, it binds to the repressor and changes

its conformation so that it is unable to bind to the operator. This allows

for expression of the operon.

The lac operon is a negatively controlled inducible operon, where the

inducer molecule is allolactose.

In negative repressible operons, transcription of the operon normally

takes place.

The trp operon, involved in the synthesis of tryptophan (which itself acts

as the corepressor ), is a negatively controlled repressible operon.

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With positive control, an activator protein stimulates transcription

by binding to DNA.

In positive inducible operons, activator proteins are normally

unable to bind to the pertinent DNA.

When an inducer is bound by the activator protein, it undergoes a

change in conformation so that it can bind to the DNA and

activate transcription.

In positive repressible operons, the activator proteins are

normally bound to the pertinent DNA segment.

However, when an inhibitor is bound by the activator, it is

prevented from binding the DNA.

This stops activation and transcription of the system.

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• 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.

• The lac operon is regulated by several factors including the

availability of glucose and lactose.

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Discovered in 1953 by Jacques Monod and colleagues, the trp

operon in E. coli was the first repressible operon to be

discovered.

This operon contains five structural genes:

trp E,

trp D,

trp C,

trp B, and

trp A, which encodes tryptophan synthetase.

It also contains a promoter which binds to RNA polymerase and

an operator which blocks transcription when bound to the

protein synthesized by the repressor gene (trp R) that binds to

the operator

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Eukaryotic cells have a much larger genome

Eukaryotes have much greater cell specialization

Thus eukaryotic cells contain an enormous amount of DNA that

does not program the synthesis of RNA or protein

This requires complex organization

In eukaryotes expression of gene into proteins can be

controlled at various locations

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• Synthesis of proteins is controlled right from the chromatin stage.

• Expression of gene is controlled at many steps during the process of

transcription and translation.

• Description of the control points is dealt in detail in the subsequent

slides.

1.Transcriptional control.

2.RNAprocessing control.

3.RNA transport & localisation control.

4.Translation control.

5.mRNAdegradation control.

6.Protein activator control.10/25/2014 36

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Two forms of chromatin • Euchromatin – A lesser coiled transcriptionally active region which can

be easily accessed by the RNA polymerases.

• Heterochromatin – A highly condensed transcriptionally inactive region.

The genes in this region cannot be accessed by the RNA polymerases

for active transcription.

• Ubiquitination:Ubiquitination of H2A – Transcriptional inactivation

Ubiquitination of H2B - Transcriptional activation

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• Histone modifications – These modifications

make a region of gene either transcriptionally

active or inactive.

Acetylation

• ↑Acetylation ----↓ Condensation of DNA ----- ↑

Transcription of genes in that region

Ubiquitination

Ubiquitination of H2A – Transcriptional inactivation

Ubiquitination of H2B - Transcriptional activation

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DNA methylation:is the addition or removal

of a methyl group predominantely where

cytosine bases occur consecutively.

bases occur consecutively.

DNA methylation:is the addition or removal

of a methyl group predominantely where

cytosine bases occur consecutively.

bases occur consecutively.

Methylation occurs most often in

symmetrical CG sequences.

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by HDACs and

corepressors leads to

heterochromatin formation

by HATs and coactivators

leads to euchromatin

formation

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• Eukaryotes – There are two types of promoters which are:

• Basal promoter or core promoter -These promoters reside

within 40bp upstream of the start site. These promoters are seen in all

protein coding genes.

• Upstream promoters - These promoters may lie up to 200bp

upstream of the transcriptional initiation site. The structure of this

promoter and the associated binding factors keeps varying from gene to

gene.

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Transcriptional control:… controlling when and how often a given gene isTranscribed

Figure 6. Genes can be expressed with different efficiencies. Gene A is transcribed andtranslated much more efficiently than gene B. This allows the amount of protein A in the cell to bemuch greater than that of protein B.

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Enhancers• Enhancers can be located upstream, downstream or

within the gene that is transcribed

• The binding of these enhancers with enhancer binding

proteins (transcription factors) increases the rate of

transcription of that gene to a greater extent.

• Promoters are capable of initiating lower levels of

transcription.

• Enhancers are responsible for the cell or tissue specific

transcription.

• Each enhancer has its own transcription factor that it

binds to.

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• www.wikipedia.com

• www.slideshare.com

• www.webmed.com

• www.ncbl.com

• Some articles from internet

• Some journals

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