Regulation of Gene Expression

Why do Organisms Regulate Transcription?

• Organisms tend to regulate gene to conserve resources and energy.

  • This gives them a selective advantage over cells that are unable to do.

• Natural selection would favor organisms that express only the gene whose products are needed by the cell.

• For example, E. coli is dependent on a human host for its nutrients. If the human host were to be lacking the amino acid tryptophan, the E. coli cell responds by activating a metabolic pathway that creates tryptophan from another compound.

  • If the human host gains tryptophan from eating, then the E. coli cell stops producing tryptophan, avoiding wasting resources.

    

• Cells can adjust production of certain enzymes by regulating the expression of genes encoding the enzymes.

  • Control of enzyme production occurs at the level of transcription, the synthesis of mRNA from the genes that code for these enzymes.

• A single promoter works for a RNA polymerase that will transcript for a tryptophan operon that contains multiple start and stop codons.

  • mRNA that results will be translated into 5 separate polypeptides.

    

• A key advantage of grouping genes relating in function into one transcription unit that a single “on-off switch” can control all of their genes.

What are Operators and Operons?

• The on-off switch is a segment of DNA called an operator.

  • It is the segment of nucleotides near the start of an operon to which an active repressor can attach to.

  • The binding of the repressor prevents RNAP from attaching onto the promoter and start transcribing.

  • Controls the access of RNAP to the genes.

• Operon is basically the system consisting of the operator, promoter, and the genes they control.

• There is the on and off switch for the operator.

  • Can be turned off by a protein called trp repressor.

  • Repressors bind to the operator, preventing RNA polymerase from transcribing the genes by not allowing it to bind.

  • A repressor protein is specific for the operator of a particular operon.

    

• Repressor proteins are coded by a regulatory gene.

  • Regulatory genes controls the transcription of another gene or group of genes.

• Most regulatory genes are allosteric proteins, with 2 alternative shapes: active and inactive.

• Corepressors are small molecules that bind to the repressor protein.

  • They change the protein’s shape, allowing the repressor to bind to the operator and switch an operon off.

• An example is tryptophan, which also functions as a corepressor.

  • As tryptophan accumulates, more tryptophan molecules associate with trp repressor molecules.

  • This can bind to the trp operator and show down production of the tryptophan pathway enzymes.

  • If there’s less tryptophan, then fewer trp repressor proteins would have tryptophan allosterically bind to it, making them inactive, allowing for the transcription of the operon to continue.

    

• Opposite of a corepressor is an inducer. They bind to the repressor proteins and inactive them, preventing them from binding to the operator.
  (IMPORTANT)
  Inducers inactivate the repressor protein, turning on transcription.

  Repressors activate the repressor protein, turning off transcription.

What are the Repressible and Inducible Operons?

• Repressible operons are operons whose transcription can be inhibited (repressed) when a specific molecule binds allosterically to a regulatory protein.

  • Ex. trp operon and tryptophan (specific molecule)

  • Operon is active by nature but repressor protein is inactive

  • When the specific molecule binds allosterically to the regulatory protein, then it activates the protein, which allows for the regulatory protein to bind to the operator.

  • This activates the repressor protein, not allowing for transcription to happen.

    

  • The trp operon is normally active because the cell constantly needs tryptophan for protein synthesis.

  • It is controlled by the trp repressor, which is inactive by itself.

  • When tryptophan levels are high, tryptophan acts as a corepressor by binding to the trp repressor and activating it.

  • The active repressor binds to the operator, blocking transcription.

  • This prevents unnecessary production of tryptophan when enough is already available.

• An Inducible operon are operons whose transcription needs to be activated (induced) when a specific molecule interacts with the regulatory protein.

  • Ex. lac operon and lactose (specific molecule)

  • Operon is inactive by nature but repressor protein is active

  • When specific molecule binds allosterically to the regulatory protein, then it inactivates the protein, not allowing for the regulatory protein to bind to the operator.

  • This deactivates the repressor protein, allowing for transcription to happen.

    

  • The lac operon controls the production of enzymes that break down lactose.

  • It is controlled by the lac repressor, which is active by default and binds to the operator, blocking transcription.

  • This means the operon is normally OFF because there is no need to make enzymes if lactose is absent.

  • When lactose is present, a small molecule called allolactose (inducer) binds to the lac repressor, inactivating it.

  • Without the active repressor, RNA polymerase can transcribe the lac genes, leading to the production of β-galactosidase and other enzymes to digest lactose.

• Enzymes of the lactose pathway are referred to as inducible enzymes b/c their synthesis is induced by a chemical signal.

  • Only produced when needed

• Repressible enzymes usually function in anabolic pathways, which synthesize essential end products from raw materials (precursors).

  • Always produced unless corepressor turns them off

  • Transcription is only turned off when the corepressor is abundant.

    

What is Positive and Negative Gene Regulation?

• Negative gene regulation involves a repressor protein that binds to the operator to BLOCK transcription.

  • Gene is normally on, but can be turned off.

  • Example is repressible and inducible operons.

• Positive gene regulation involves an activator protein that binds to DNA to INCREASE transcription.

  • Turns on or enhances gene expression

  • Example is cAMP and CAP.

• Only the lac operon is regulated through both negative and positive gene regulation.

  

• Another allosteric regulatory molecule is cyclic AMP (cAMP).

  • cAMP accumulates when glucose is scarce, but decreases when there is high concentrations of glucose.

  • If the amount of glucose in the cell increases, the cAMP concentration falls, and without cAMP, CRP detaches from the operon.

• The regulatory protein cAMP receptor protein (CRP) is an activator, and it binds to DNA an stimulates the transcription of a gene.

  • An activator is a protein that binds to DNA to stimulate gene transcription.

  • In prokaryotes, activators bind in or near the promoter.

  • In eukaryotes, activators bind to control elements in enhancers.

• When cAMP binds to CRP, CRP becomes activated and there can attach to a specific site upstream from the lac promoter.

• This attachment increases the affinity of RNAP for the lac promoter.

• This binding increases RNAP’s transcription of genes, so it is considered positive regulation.

How else can Gene Expression be Regulated?

• Both unicellular organisms and the cells of multicellular organisms continually turn genes on and off in response to signals from their external and internal environments.

• To perform its own distinct role, each cell type must maintain a specific program of gene expression in which certain genes are expressed and others are not.

• The differences between cell types, therefore, are due not to different genes being present

  • But it is actually due to differential gene expression, the expression of different genes by cells with the same genome.

    

• Gene regulation, in eukaryotes, not only takes place in transcription, but also in different stages as well.

• Another way is the regulation of chromatin structure.

  • Chromatin is the basic unit of nucleosomes.

  • Packs a cell’s DNA into a compact form that fits inside of the nucleus.

  • Also helps regulate gene expression in several ways.

• Whether or not a gene is transcribed is affected by the location of nucleosomes along a gene’s promoter and also the sites where the promoter DNA attaches to the protein scaffolding of the chromosome.

• Lastly, chromatin structure and gene expression can be influenced by chemical modifications to the histone proteins and DNA nucleotides.

  

• The N-terminus of each histone protein in a nucleosome protrudes outward from the nucleosome.

  • These so-called histone tails are accessible to various modifying enzymes

  • These enzymes catalyze the addition or removal of specific chemical groups, such as acetyl , methyl, and phosphate groups.

• Histone acetylation promotes transcription by opening up the chromatin structure.

  • It is the addition of an acetyl group to an amino acid in a histone tail.

    

• The process of DNA methylation involves the addition of a methyl group (–CH₃) to specific bases in the DNA, typically cytosine.

  • Methylated DNA is generally associated with gene silencing, meaning that genes in heavily methylated regions are less likely to be expressed.

  • Once methylated, genes usually stay that way through successive cell divisions in a given individual.

  • Once methylated, genes usually stay that way through successive cell divisions in a given individual.

  • At DNA sites where one strand is already methylated, enzymes methylate the correct daughter strand after each round of DNA replication.

  • In this way, methylation patterns can be inherited.

• Inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself is called epigenetic inheritance.

  • The study epigenetic inheritence is called epigenetics.

    

• Whereas mutations in DNA are permanent, modifications to the chromatin can be reversed.

  • Furthermore, they are changeable, thus responding more rapidly to environmental conditions.