Ch. 7: Regulation of Gene Expression in Prokaryotes I

The human body contains many different cell types, but they share the same genomic sequence. How can cells with the same genome develop and maintain such different identities and functions?

These differences do not arise from the differences in the DNA sequence itself, but from differences in which genes are turned on or off, when they are expressed, and at what levels. This depends on the regulation of gene expression.

Are all gene regulated?

yes, but not in the same way

gene expression

the process of turning on a gene to produce RNA and protein

What are the 2 ways genes are expressed?

constitutively and under specific conditions

constitutively expressed

constitutively stressed in cells under all conditions, because their products are needed for basic cellular functions and viability in all conditions

ex. the proteins or enzymes that make energy are constitutively expressed, because we always need energy

regulated genes

Genes that are expressed under specific conditions, because they’re often only required for specialized functions rather than basic viability.

They are not always needed, but can provide a fitness advantage under specific conditions.

Ex. genes induced by heat stress can help cells survive elevated temperatures

Prokaryotes gene expression is controlled at what level(s)?

transcriptional level

When more protein is needed, transcription increases.

When the protein is no longer needed, transcription decreases or stops.

Eukaryotes gene expression is controlled at what level(s)?

at all stages of the process

What multiple levels are regulated in eukaryotic gene expression?

1. epigenetic level

2. transcriptional level

3. post-transcriptional level

4. translational level

5. post-translational level

epigenetic level

when DNA is uncoiled and loosened from nucleosomes to bind transcription factor (DNA is only recognized by RNA polymerase when it is unpackaged)

transcriptional level

when the RNA is transcribed

post-transcriptional level

when the RNA is processed, exported to the cytoplasm, or selectively degraded after it is transcribed

translational level

when the RNA is translated into protein

post-translational level

after the protein has been made

In prokaryotes, genes with related functions—such as the genes that encode the enzymes catalyzing the many steps in a single biochemical pathway— are regulated together and found where?

next to each other on the DNA

What do the cluster of genes shown in the image share?

1 promoter and regulatory sequence that control the transcription unit

The promoter has simultaneous control over what?

the regulation of the transcription of the structural genes, because they will either all be needed at the same time, or none will be needed

What is the benefit of grouping related genes under a common control mechanism?

it allows bacteria to rapidly adopt to changes in the environment

What are the 3 major components of an operon?

1. structural genes

2. regulatory region

3. regulatory gene

structural genes

encode proteins involved in metabolism, biosynthesis, or cellular structure

regulatory region

includes the promoter and the region surrounding the promoter, to which transcription factors, proteins encoded by regulatory genes, can bind

regulatory gene

• encode regulatory proteins (repressors and activators)

• transcription of these genes is under the control of its own promoter but often found next to the operon on the same DNA

True or False: The regulatory gene has its own operator.

True

True or False: Both the repressor and activator bind to the operator.

False. The operator is only a place for a repressor to bind, not the activator.

transcription factors

influence the binding of RNA polymerase to the promoter and allow its progression to transcribe structural genes

What are the 2 types of transcription factors?

repressor and activator

Which of these is not a protein: repressor, activator, inducer?

inducer. it is a small molecule

repressor

a transcription factor that suppresses transcription in response to an external stimulus

How does a repressor work?

Binds to a DNA sequence within the regulatory region called the operator, which is located between the RNA polymerase binding site of the promoter and the transcriptional start site of the 1st structural gene.

Repressor binding physically blocks RNA polymerase from transcribing structural genes.

Activator

a transcription factor that increases the transcription of a gene in response to an external stimulus by facilitating RNA polymerase binding to the promoter (usually upstream of the promoter)

inducer

A small molecule that either activates or represses transcription by interacting with a repressor or an activator. It is not a transcription factor.

How does one transcript code for multiple proteins?

Just like DNA replication and transcription have different start and stop signal, translation also has its own start and stop signals

Where does translation begin and end?

It begins at the translation start codon (AUG) and ends at the translation stop codon (UAA, UAG, or UGA) on mRNA

open reading frame (ORF)

the region between the start codon and stop codon

leader sequence

5’ untranslated region, or 5’ UTR located at the 5’ end of mRNA. Contains a ribosome-binding site (RBS)

ribosome-binding site (RBS)

allows the ribosome to bind to the mRNA and initiate translation

The ribosome-binding site (RBS) is similar to what?

This is similar to the promoter on DNA, which allows RNA polymerase to bind and signals where mRNA transcription begins

A polycistronic mRNA contains one ORF or multiple ORFs within a single mRNA molecule?

multiple ORFs

Each ORF has its own translation start and stop signal. What does this tell us?

one mRNA can be translated into multiple different proteins

cis-elements

DNA sequences that provide binding sites for proteins involved in transcriptional regulation.

Where are cis-elements located?

on the same piece of DNA as the gene they regulate

Promoter, operator, and activator-binding sites. Are these examples of cis-elements or trans-regulators?

cis-elements

Trans-regulators

proteins that bind cis-elements to regulate transcription

Where are trans-regulators located?

They do not necessarily need to be encoded on the same piece of DNA as the genes they regulate. They are located anywhere in the genome, often far away from or even on a completely different chromosome than the target genes they regulate

What are the types of gene regulation?

inducible operon and repressible operon

negative and positive control

inducible operon

the operon is normally OFF

• something must happen to turn it ON to induce transcription

• Often activated in response to a metabolite that regulates the operon

metabolite

a small molecule undergoing metabolism

repressible operon

the operon is normally ON.

• something must happen to turn it OFF to repress transcription

• typically regulated in response to a metabolite

negative control

the regulatory protein used is a repressor

• the operon will be turned OFF when the repressor is present

• the operon will be turned ON when the repressor is absent or inactivated

positive control

the regulatory protein used is an activator

• the operon will be turned ON when the activator is present

• the operon will be turned OFF when the activator is absent or inactivated

positive inducible operon

inducible= the operon is normally off

positive control= activator protein is used to control gene expression

The operon is normally off because the activator does not bind to the DNA.

Metabolite accumulates and binds to the activator protein, enabling it to bind to the DNA. This turns the operon ON and inducing transcription.

Negative inducible operon

inducible= the operon is normally OFF

negative control= repressor protein is used to control gene expression

The operon is normally OFF because the repressor protein is bound to the operator, preventing RNA polymerase to bind.

Metabolite accumulates and binds to the repressor protein, preventing it form binding to the DNA. This turns the operon ON and inducing transcription.

Positive repressible operon

repressible= operon is normally ON

positive control= activator protein is used to control gene expression

The operon is normally ON because the activator protein is present and binds to the DNA.

Metabolite accumulates and binds to the activator protein, preventing it from binding to the DNA. This turns the operon OFF and repressing transcription.

negative repressible operon

repressible= the operon is normally ON

negative control= repressor protein is used to control gene expression

The operon is normally ON because repressor protein does NOT bind to the DNA.

Metabolite accumulates and binds to the repressor protein, enabling it to bind to the DNA. This turns the operon OFF and repressing transcription.

In a positive inducible operon, what is the normal state of transcription when the inducing

metabolite is absent?

A. Transcription is ON at a high level

B. Transcription is OFF or very low

C. Transcription alternates between ON and OFF

D. Transcription is independent of the activator

B. Transcription is OFF or very low

What type of operon is represented by the schematic?

A. Positive inducible operon

B. Negative inducible operon

C. Positive repressible operon

D. Negative repressible operon

A. Positive inducible operon