Regulation and Gene Expression

Bacteria vs. Eukaryotes

• Both alter their patterns of gene expression in response to changes in environmental conditions– This regulation often happens during transcription

Bacterial Gene Expression• Can conserve resources & energy based on a change in their environmentEX: E. coli in colon

IF environment lacks the A.A. tryptophan (which is essential for E. coli survival) then metabolic pathway to make tryp. is triggered in bacteria

BUT if host eats big thanksgiving turkey, the bacteria stop making tryp. and conserve energy

SO… Bacteria cells can adjust

1. activity of enzymes already present

There is a ceiling… IF too much is already present it blocks more f/ being made

2. production levels of certain enzymes

Occurs at transcription level = genes can be switched ON or OFF

= controlled gene expression

Operon ModelA mechanism for controlling gene expression

• A set of enzymes cause reaction w/ a certain gene coding for each enzyme produced

*each enzyme “gene” is really 1 long mRNA strand/gene with multiple start/stop codons = 5 separate polypeptides produced f/ 1 transcription unit

Advantage = a single ON/OFF switch can control the entire pathway!

Operon ModelA mechanism for controlling gene expression

This ON/OFF switch is a segment of DNA called an

OPERATOR = located in promoter and controls RNA polymerase access to genes

All together… the entire length of DNA (operator, promoter, and genes) are called an OPERON

The operon for tryptophan pathway is called trp operon … 1 of many operons in the bacterial genome

So how does ON/OFF switch work?

• By itself, trp operon is ON BUT can be switched off by protein called trp repressor, which binds to operator and blocks binding of RNA polymerase to promoter

• Repressors are specific to operons

Why not switched off permanently?• FIRST: Binding of repressor is reversible

– Duration of binding or not binding of repressor depends on amount of active repressor proteins around

• SECOND: Trp repressor is an allosteric protein – alternating between shapes (active vs. inactive)– Only if tryptophan binds to trp repressor at allosteric site does repressor

proteins become active attaching to operator and turning operon off Tryptophan acts as a co-repressor

Lac operon • Inducible operon (in contrast w/ trp repressor

operon)

Lac operon• Designed for E.coli to help

break down lactose • Lactose binds to repressor = changes shape repressor no

longer can bind to operon gene gets transcribed to protein that breaks down lactose

• If increase lac amount in environment, lactose protein made to help break it down

• If NO lactose present, operator in OFF position b/c repressor is ACTIVATED and sitting in operator = no gene transcribed

“PROG”: Promoter, repressor,

operator, gene

Eukaryotic Gene Expression

• Contain many different types of cells– On average, a typical human cell

expresses only 20% of its genes w/ highly differentiated cells expressing less!

• Although they all contain the same genome, their specific gene expression allows these cells to be unique in function

DIFFERENTIAL GENE EXPRESSION

Differential Gene Expression• Every stage is a potential point at which gene expression can be turned ON or

OFF, accelerated or slowed down A common control point is transcription

BUTThe complexity of a euk. cell allows for controlled gene expression at many different stages

1. Target DNA – pre-transcription2. Target RNA – post-transcription 3. Target Protein – post-translation

Target DNA

• Remember… How is DNA packaged?

• Let’s draw– Label: histone,

DNA, nucleosome, and N-terminus tail of histone

Target DNA

• HISTONE modifications can affect gene transcription– N-terminus tail is easily accessible to modifying

proteins that add or remove chemical groups

Target DNA• HISTONE modifications:

A. HISTONE ACETYLATION – acetyl groups (-COCH3) are attached to lysines in histone tails = neutralization of lysine positive charge

NO binding to neighboring proteins = loose chromatin structure = easy access to genes

Target DNA• HISTONE modifications:

B. DNA METHYLATION – enzymes add methyl groups (-CH3) to certain bases in DNA (usually C)

studies show genes of a cell that are heavily methylated are these genes that are not being expressed

Target DNA• SUMMING UP HISTONE modifications:

A. HISTONE ACETYLATION = loosens chromatin increase transcription of gene

B. B. DNA METHYLATION = blocks transcription of gene

Target RNA RNA interference (RNAi)1993 discovery – small single stranded RNA molecules called microRNA (miRNAs) that can bind to mRNA as its compliment and either degrade the mRNA or block it from translation

Estimated that at least ½ of human genes may be regulated by miRNAs or siRNAs (double stranded silencing RNA)

Target Protein

• Selective degradation = controls how much time a specific protein is functioning in the cell– EX: cyclins must be short lived… so they must be

marked for destruction!Small proteins called ubiquitins attach to the

protein Giant protein complexes called proteasomes then

recognize ubiquitin tagged proteins and degrade them

Target Protein

• FUN FACT! In 1994 3 scientists were awarded the Nobel Prize for finding specific mutations in cell cycle proteins and concluded that these mutations can cause these proteins to be impervious to proteasome degradation and can therefore cause cancer!