Gene regulation in prokaryotes Gene regulation in prokaryotes and eukaryotesand eukaryotes

Year 13Year 13

EnzymesEnzymes Are biological catalysts.Are biological catalysts.

Speed up the chemical reactions in living Speed up the chemical reactions in living organisms.organisms.

Without enzymes, the chemical reactions of life Without enzymes, the chemical reactions of life would proceed so slowly that life would be would proceed so slowly that life would be hardly possible.hardly possible.

Are not used up or changed by the reaction.Are not used up or changed by the reaction.

What are enzymes What are enzymes made of?made of?

Chemically, enzymes are proteins.Chemically, enzymes are proteins.

Because of the unique shape of each Because of the unique shape of each enzyme it is specific to a particular enzyme it is specific to a particular reaction – it will catalyse only one reaction.reaction – it will catalyse only one reaction.

There areThere are,, therefore therefore,, thousands of thousands of different enzymes in any living organism.different enzymes in any living organism.

Some Some definitions:definitions:

Substrate: the chemicals an enzyme acts Substrate: the chemicals an enzyme acts on.on.

Active site: the part of the enzyme where Active site: the part of the enzyme where the substrate binds and where the reaction the substrate binds and where the reaction occurs. The active site has a specific occurs. The active site has a specific shape so only specific substrates can bind.shape so only specific substrates can bind.

Nomenclature: aseNomenclature: ase

How do enzymes work?

2 models: lock and key

induced fit

See page 95 Biozone

MetabolismMetabolism Is all the chemical reactions that occur in the cell of an Is all the chemical reactions that occur in the cell of an

organism. organism.

Metabolism is made up of all the different processes an Metabolism is made up of all the different processes an organism needs to maintain itself such as growth, organism needs to maintain itself such as growth, energy, repair, and excretion. energy, repair, and excretion.

These processes are a complex network of metabolic These processes are a complex network of metabolic pathways which are controlled by enzymes. pathways which are controlled by enzymes.

The importance of The importance of enzymes in metabolic enzymes in metabolic

pathways.pathways. A metabolic pathway is a series of “steps” from A metabolic pathway is a series of “steps” from

a starter molecule, resulting in the formation of a starter molecule, resulting in the formation of a different end product. Many intermediate a different end product. Many intermediate compounds can be formed in the pathway. compounds can be formed in the pathway.

Each step in the pathway is controlled by an Each step in the pathway is controlled by an enzyme.enzyme.

A faulty enzyme can cause metabolic disorders.A faulty enzyme can cause metabolic disorders.

Metabolic pathways can be:

anabolic: produce large molecules from smaller ones or

catabolic: break large molecules into smaller ones.

Phenylalanine

Tyrosine

Hydroxyphenylpyruvic acid

Homogentisic acid

Maleyacetoacetic acid

CO2 and H2O

MelaninThyroxine

Enzyme A

Enzyme BEnzymesEnzyme C

Enzyme D

Enzyme E

Enzyme F

Metabolism of phenylalanine

Do exercises Page 97 and 98

Control of gene expression Control of gene expression in metabolic pathwaysin metabolic pathways

Gene expression of enzymes in a metabolic Gene expression of enzymes in a metabolic pathway must be tightly controlled so the cell has pathway must be tightly controlled so the cell has the correct amount of each enzyme it requires. the correct amount of each enzyme it requires. Control often occurs at transcription.Control often occurs at transcription.

Some genes are induced – they are only switched Some genes are induced – they are only switched on in certain situations.on in certain situations.

Other genes are transcribed continuously because Other genes are transcribed continuously because their products are always needed eg genes coding their products are always needed eg genes coding for respiratory enzymes.for respiratory enzymes.

Gene regulationGene regulation

Two types of genes:Two types of genes:

1)1)Structural genes – encode specific Structural genes – encode specific proteinsproteins

2)2)Regulatory genes – control the Regulatory genes – control the level of activity of structural genes level of activity of structural genes ie. Control structural gene ie. Control structural gene expression.expression.

Gene regulation in Gene regulation in prokaryotesprokaryotes

In prokaryotes, operons control the In prokaryotes, operons control the rate of transcription.rate of transcription.

An operon is a group of genes that An operon is a group of genes that work together and code for the work together and code for the enzymes regulating a particular enzymes regulating a particular metabolic pathway.metabolic pathway.

Regulator gene

Promoter OperatorStructural gene A

Produces the repressor

RNA polymerase binding site

Repressor binding site

OPERON

Structural gene B

Structure of the operonStructure of the operonThe operon in prokaryotes comprises a The operon in prokaryotes comprises a

number of different features:number of different features:

1)1) Structural genes: code for particular Structural genes: code for particular enzymes in a metabolic pathwayenzymes in a metabolic pathway

2)2) Promoter gene: recognition site for the Promoter gene: recognition site for the RNA polymerase to bind to.RNA polymerase to bind to.

3)3) Operator gene: controls the production Operator gene: controls the production of mRNA from structural genes.of mRNA from structural genes.

INDUCTION

R P O SG1 SG2R

If a substrate is uncommon the bacteria will not need the enzymes most of the time. So the repressor is usually attached.

This prevents RNA polymerase from forming mRNA. Therefore: no enzymes.

When the substrate molecule is present some of it acts as an inducer; it binds to the repressor, changing its shape so it can’t bind to the DNA.

Transcription takes place.

R

R

Inducer

See this movie on the Lac operon in E. coli

for more detail

REPRESSION

When a substrate is normally present the enzyme should be normally operating. The only time this should stop is when the end product levels build up too much.

The repressor cannot bind to the operator.

Some of the excess product acts as an effector, which helps the repressor to bind.

Transcription is stopped.

R P O SG1 SG2RR

R

See this movie on the Tryp operon in E. coli

for more detail

http://www.sumanasinc.com/webcontent/anisamples/majorsbiology/lacoperon.html

Lac Operon - induction:

Lac gene off (normal state)

Lactose present- acts as an inducer.

Lactose binds to the repressor protein.

Repressor can’t bind to the operator.

RNA polymerase binds . Lac gene on. Structural proteins made.

Repressor molecule binds to operator and prevents transcription by RNA polymerase

Tryptophan operon - repression

Tryp gene on (normal state)

Tryptophan accumulates in excess. Some of it acts as an effector and activates the repressor molecule.

Effector and repressor molecule bind to the operator gene and prevent transcription by RNA polymerase.

Tryptophan levels in cells decrease, no excess.

Tryptophan doesn’t bind to the repressor which then can’t bind to the operator.

RNA polymerase binds

Lactose all used up.

Gene regulation in Gene regulation in prokaryotes - prokaryotes -

summarysummary Genes for a metabolic pathway are linked Genes for a metabolic pathway are linked

together in operons with a common switch together in operons with a common switch mechanism (operator).mechanism (operator).

No introns – no RNA processingNo introns – no RNA processing

The structural genes undergo transcription The structural genes undergo transcription and translation simultaneously.and translation simultaneously.

Regulation occurs by switching all genes of a Regulation occurs by switching all genes of a pathway on or off.pathway on or off.

Gene regulation in Gene regulation in eukaryoteseukaryotes

Genes for metabolic pathways in eukaryotic cells Genes for metabolic pathways in eukaryotic cells are separated, not grouped as operons.are separated, not grouped as operons.

The genes for a metabolic pathway are switched The genes for a metabolic pathway are switched on separately.on separately.

Genes have introns that are removed in RNA Genes have introns that are removed in RNA processing.processing.

Eukaryotic genes have a relatively large number Eukaryotic genes have a relatively large number of control elements.of control elements.

Regulatory DNA Regulatory DNA regionsregions

Eukaryotic genes have a promoter region Eukaryotic genes have a promoter region upstream of the coding region, where RNA upstream of the coding region, where RNA polymerase binds.polymerase binds.

There are 2 two types of regulatory sequences There are 2 two types of regulatory sequences that effect transcription of the structural gene:that effect transcription of the structural gene:

1) enhancer 1) enhancer 2) silencer 2) silencer

These are located upstream, downstream or These are located upstream, downstream or within the gene (in introns).within the gene (in introns).

Enhancer sequencesEnhancer sequences

These are non-protein-coding sections of These are non-protein-coding sections of DNA that help regulate transcription by DNA that help regulate transcription by binding proteins called transcription binding proteins called transcription factors.factors.

Silencer sequencesSilencer sequences

These are non-protein-coding sections of These are non-protein-coding sections of DNA that help regulate transcription by DNA that help regulate transcription by binding proteins called repressors.binding proteins called repressors.

Transcription factorsTranscription factors

Two types: Two types: 1) Activators – these are small proteins 1) Activators – these are small proteins

that bind to enhancer sequences or RNA that bind to enhancer sequences or RNA polymerase. They cause an increase in polymerase. They cause an increase in transcription.transcription.

2) Repressors – these are small proteins 2) Repressors – these are small proteins that bind to silencer regulatory genes. that bind to silencer regulatory genes. They cause a decrease in transcription.They cause a decrease in transcription.

Coding region of gene

Promoter region of DNA

RNA polymerase Transcription factors that

bind to RNA polymeraseTranscription factors

(activators) that bind to

the enhancer sequence

Enhancer sequence

of DNA

Role of Role of Transcription Transcription

FactorsFactors

Eukaryotic RNA polymerase cannot, on its own, initiate transcription.

It depends on transcription factors to recognize and bind to the promoter.

Transcription factors also bind to the enhancer sequence of DNA

Transcription factors that

bind to RNA polymerase

Coding region of geneEnhancer

sequence of DNA

Transcription factors

(activators) that bind to

the enhancer

Promoter region of DNA

RNA polymerase

Activating Activating TranscriptionTranscription

Transcription is activated when a hairpin loop in the DNA brings the

transcription factors on the enhancer sequence (activators) in contact

with the transcription factors bound to the RNA polymerase at the promoter.

Protein-protein interactions are crucial to eukaryotic tanscription.

The RNA polymerase can only produce a mRNA molecule once the complete

initiation complex is assembled.

Enhancer Promoter

RNA polymerase

ActivatorsTranscription factors

bound to RNA polymerase

Initiation complex

Transcription proceeds

until a terminator

sequence is encountered.

Then transcription stops.

http://highered.mcgraw-hill.com/ohttp://highered.mcgraw-hill.com/olc/dl/120080/bio28.swflc/dl/120080/bio28.swf

DEFECTIVE GENES

Cell division is tightly controlled. If a cells DNA becomes damaged a gene (p53) within the cell causes cell division to cease until it is repaired. Other genes (proto-oncogenes) allows cell division to begin.

If DNA damage is irreparable or cells get too old they self destruct, called apoptosis.

If damage occurs in either of the 2 genes mentioned above the cell will grow at an uncontrolled rate, or become effectively immortal.

These cells cease to carry out normal functioning. If the damage is not too severe the cells may form a benign tumour. If many genes are affected the tumour is said to be cancerous.

Lab manual page 99