control of gene expression bio 329\

All cells of a multicellular organism contain the same

Genome

What is a genome

An entire set of DNA of an organism

All cells posses the same genome but express only the

RNA and proteins specific for that cell type (differentiation)

Differentitated cells contain all the

Genetic information of the organism

Difference cell types produce different set of

Proteins

Many proteins are common to all cells of a

Multicellular organism

Housekeeping proteins used for

Common functions of cells

Each cell type also produces

Specialized proteins that are responsible for the cell’s distinctive properties

Eukaryotic cells can control which proteins they contain by

regulating various steps along the pathway to gene expression.

most genes the main site of control is

step 1: transcription of a DNA sequence into RNA.

Many proteins require what to become fully activated

Post translational modifications

Transcription regulator binds to

Regulatory DNDA sequences

How is transcription regulated

Through activators, repressors, and inducers

Repressors turn genes

Off

Activators turn genes

On

Repressors and activators

are proteins that bind DNA and regulate expression

Inducers and co-Repressors are small molecules that may participate in

Gene regulation by altering the function of repressors and activators

Prokaryotic genes are often organized into

Operó a

Operons are

Cluster of genes that are transcribed as a single unit

Operon allow regulation of

Expression of The entire cluster through a single transcription switch

Switches allow cells to respond to changes in their

Transcription environment

A cluster of bacterial genes can be transcribed from a single

Promoter

Repressor proteins regulate

Trp operon gene expression

If the concentration of tryptophan inside a bacterium is low

RNA polymerase binds to the promoter and transcribes the 5 genes of the tryptophan operon

However, if the concentration of tryptophan is high

the repressor protein becomes active and binds to the operator, where it blocks the binding of RNA polymerase to the promoter.

When the concentration of intracellular tryptophan drops, the repressor falls off the

DNA, allowing the polymerase to again transcribe the operon. The promoter contains two key blocks of DNA sequence information, the –35 and –10 regions,

The -10 and -35 regions are recognized by

RNA polymerase

Activate the repressors making it bind to the operator

The lac operon is controlled by two transcription regulators:

The lac repressor and CAP

When lactose is absent, the Lac repressor binds to the

LAC operator and shuts off expression of the operon

allolactose binds to the Lac repressor, causing it to undergo a conformational change that releases

 its grip on the operator DNA

When glucose is absent cyclic AMP and CAP does what?

Cyclic AMP is produced by the cell and CAP binds to the DNA

For the operon to be transcribed, glucose must be

Absent and lactose must be present

LacZ, the first gene of the operon, encodes the enzyme

β-galactosidase, which breaks down lactose into galactose and glucose

Inactivate the repressors, making it leave the operator

Transcription is controlled by

Proteins binding regulatory DNA sequences

Regulatory proteins are

Specific transcription factors

Regulatory proteins bind DNA and either stimulate or inhibit the

RNA polymerase

Regulatory proteins binding are achieved by interactions between

Protein and DNA

In enkaryotes, gene activation can occur at a

Distance

An activator protein bound to a distant enhancer attracts

 RNA polymerase and the general transcription factors to the promoter.

 Looping of the intervening DNA permits contact between the

activator and the transcription initiation complex bound to the promoter.

The arrangement of chromosomes into looped domains keep Enhancers

In check

Eukaryotic genes are controlled by

Combinations of transcription regulators

DNA sequences may play a structural role in allowing the regulatory DNA sequences to find their proper positions, but they are not recognized by any

Transcription regulators

GTF recruits RNA pol II to all promoters, while specific TF regulate subsets of genes

Combinations of a few transcription regulators can generate

Many cell types during development

The expression of different genes can be coordinated by a single

Protein

Interphase chromosomes contain both highly condensed and more extended forms of

Chromatin called euchromatin and heterochromatin

Euchromatin

Extended, more loosely package, accessible for gene expression

Heterochromatin

Tightly package, not expressed

Facultative heterochromatin are

Regions of tightly packaged DNA that can be modified to switch to euchromatin

Constitutive heterochromatin are

Always tightly packed, not expressed, often in structural regions of the chromosomes

Eukaryotic transcriptional activators can recruit chromatin-modifying proteins to help

initiate gene transcription

What are the mechanism of gene regulation by TF

Coactivators and corepressors

TFs can recruit

Histone acetlytransferanse (HATs)

HATs add acetylene groups to

Lysines in histone tails

Histones acetylation reduces the affinity of

Histones to DNA

Gene activation allows Transcriptional machinery to access

DNA

In general silencing TFs recruit

Histone deacetylase (HDACs)

HDACs remove acetylene groups from

Histones

Gene silencing silences

Gene expression

In DNA methylation the addition of a methyl group is added on the

5’-C of cytosine base

DNA methylation is carried out by

DNA methyltransferases

Up to 10% of the cytosines in vertebrates are

Methylated

DNA methylation leads to

Gene silencing

Methylated promoters are less likely to bound by

PIC proteins

DNA methylation patterns can be faithfully inherited when a cell

Divides

An enzyme called a maintenance methyltransferase guarantees that once a pattern of DNA methylation has been established, it is inherited by

 newly synthesized DNA

Immediately after DNA replication, each daughter double helix will contain

 one methylated DNA strand—inherited from the parent double helix—and one unmethylated, newly synthesized strand

 The maintenance methyltransferase interacts with these hybrid double helices and methylates only those

 CG sequences that are base-paired with a CG sequence that is already methylated

Cytosine ca be methylated in

DNA

mRNAs Contain Sequences That Control Their

Translation

Regulatory RNAs Control the Expression of Thousands of

Genes

MicroRNAs Direct the Destruction of

Target mRNAs

Small interfering RNAs protect cells from

Infections

Bacteria use small non coding RNAs to protect themselves form

Viruses

Thousands of Long Noncoding RNAs May Also Regulate

Mammalian Gene Activity

Eukaryotic genes contain many

Exons

mRNA can retain all or splice some of __ out

Exons

In alternative splicing the same gene can produce different

mRNAs

Splicing pathways may depend on the

Stage of development, cell type, and tissue type

bacterial gene’s expression can be controlled by

Regulating translation of its mRNA

Sequence-specific RNA-binding proteins can repress the translation of specific mRNAs by

keeping the ribosome from binding to the ribosome-binding sequence in the mRNA

If a ribosomal protein is accidentally produced in excess over other ribosomal components, the free protein will

inhibit translation of its own mRNA, thereby blocking its own synthesis.

As new ribosomes are assembled, the levels of the free protein

Decrease, allowing the mRNA to again be translated and the ribosomal protein to be produced

An miRNA targets a complementary mRNA molecule for

Destruction

Each precursor miRNA transcript is processed to form a double-stranded intermediate, which is further processed to form a

mature, single-stranded miRNA

miRNA assembles with a set of proteins into a complex called

RISC, which then searches for mRNAs that have a nucleotide sequence complementary to its bound miRNA

Depending on how extensive the region of complementarity is, the target mRNA is either rapidly

degraded by a nuclease within the RISC or transferred to an area of the cytoplasm where other nucleases eventually destroy it

Preston’s may be selectively targeted for degradation when there are

Misfolded or damaged proteins and regulatory proteins that need to be removed

Proteins destined for degradation are labeled with

Ubiquitin; a small protein

Ubiquitinated proteins bind to the cap of

Proteasome, a huge proteolytic complex

Proteins are sucked in to the

Proteasome and is destroyed

It allows cell types and signal specific gene regulation using limited TFs

What are the importance of regulation of gene expression

By altering gene expression, organisms can adapt to environmental challenges.

Transcription control can result in tissue specific gene expression.

Gene regulation is influenced by hormones, heavy metals and chemicals.

Dysregulation of gene regulation can lead to disease.