Lecture 4 (Chapter 16): Regulation of gene expression

Key concepts

• prokaryotic gene expression is regulated in operons

• eukaryotic gene expression is regulated by transcription factors

• epigenetic changes regulate gene expression

• eukaryotic gene expression can be regulated after transcription

Two ways to regulate a metabolic pathway

1. Allosteric regulation

2. Regulation of protein synthesis

Allosteric regulation

regulation of enzyme-catalyzed reaction (enzyme activity) allows rapid fine-tuning

Regulation of protein synthesis

slower regulation but conserves energy and resources since protein synthesis requires a log of energy (transcription regulation via regulation of enzyme concentration)

Alternative method for controlling an enzyme/cell function

acetylation, methylation, phosphorylation

Where is prokaryotic gene expression regulatied?

in operons

Do all promoters have the same recognition sequences?

No! different classes of promoters have different recognition sequences (ex. -35 and -10)

What must happen before transcription can begin?

• DNA sequence binds RNA pol and sigma factors to enhance RNA pol binding at certain promoters

• RNA pol by be bound to sigma factor before it can recognize a promoter and begin transcription

What is Sigma-70?

a sigma factor that is active most of the time and bins to recognition sequences of housekeeping genes (genes normally expressed in actively growing cells)

What is an example of an enzyme that can induce the expression of specific gene(s)?

lactose! In e. coli the intestine must adjust quickly to changes in food supply. When lactose is added, mRNA for the enzyme is made, once it’s removed, the amount of mRNA is decreased

Two types of prokaryotic gene regulation

1. inducible systems

2. repressible systems

inducible systems

substrate (inducer) interacts with a regulatory protein (repressor); repressor can’t bin to operator and transcription proceeds

repressible systems

a product (co-repressor) binds to a regulatory protein, which then binds to the operator and blocks transcription

What is regulated gene expression in prokaryotes?

prokaryotes made some proteins only when they are needed through transcription regulation. regulatory proteins bind to promoters

Negative regulation

a repressor protein prevents transcription (without, doing transcription)

positive regulation

an activator protein stimulates transcription (without, not doing transcription)

What type of system is the lac operon?

it is an inducible system (can be turned on)

Operon

gene cluster with a single promoter

What does an operon consist of?

• a promoter

• two or more structural genes

• an operator (short DNA sequence between promoter and structural genes that binds to regulatory proteins)

Structural genes

specify a primary protein structure (the amino acid sequence). Three structural genes for lactose enzyme are adjacent to the chromosome and share a promoter

Lac operon

• the repressor has two binding sites, one for the operator (actual DNA sequence in operon), and one for the inducer (allolactose; small molecule that binds to repressor)

• When lactose is absent, the repressor prevents binding of RNA polymerase to the promoter which blocks transcription

trp operon

a repressible system that is always on unless repressed

• the genes code for enzymes that catalyze synthesis of tryptophan

• when there is enough tryptophan in the cell, tryptophan binds to the repressor which then binds to the operator

• tryptophan is a co-repressor (helps shut down gene expression but doesn’t bind to operon directly)

What regulates eukaryotic gene expression?

transcription factors! expression of eukaryotic genes must be precisely regulated, which can occur at several different points

Eukaryote promoters

sequences near the 5’ end of the coding region, many have a sequence called the TATA box where the DNA begins to denature. promoters also include regulatory sequences recognized by transcription factors

Regulation of RNA polymerase II binding

• RNA pol II can only bind to the promoter after general transcription factors have assembled on the chromosome

• TFIID binds to the TATA box first, then the other factors bind to form an initiation complex

• each general transcription factor has a role in gene expression

Enhancers

regulatory sequences that bind transcription factors that activate or increase the rate of transcription (positive regulation)

Silencers

bind transcription factors that repress transcription (negative regulation)

Where are regulatory sequences located in eukaryotes?

thousands of base pairs away, and may affect the expression of several nearby genes

mediator

a protein that binds to the basal transcription apparatus and causes DNA to bend, bringing regulatory sequences close to the promoter

Requirements of structural motif for DNA recognition

• must fit into a major or minor groove

• have amino acids that can project into the interior of the double helix

• have amino acids that can form hydrogen bonds with interior bases

structural motifs are a recurring protein shape that enables DNA binding or protein interaction

What mediates cell differentiation?

transcription factors that determine gene expression

Formation of muscle cells

• transcription factors fist inhibit cell division, the first step in differentiation

• other transcription factors control the other processes of differentiation

How do eukaryotes coordinate expression of sets of genes?

• most have their own promoters, and the genes may be far apart in the genome

• if the genes have common regulatory sequences, they can be regulated by the same transcription factors

Example of coordinated gene expression in plants

• plants in drought stress must make several proteins which genes are scattered throughout the genome

• each of the genes has a regulatory sequence called stress response element (SRE)

• a transcription factor binds to the SRE and this element stimulates mRNA synthesis