1. Regulation and Gene Expression

2. Bacteria vs. Eukaryotes
Both alter their patterns of gene expression in response to changes in environmental conditions
This regulation often happens during transcription

3. Bacterial Gene Expression
Can conserve resources & energy based on a change in their environment
EX: 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

4. SO… Bacteria cells can adjust
activity of enzymes already present
There is a ceiling… IF too much is already present it blocks more f/ being made
production levels of certain enzymes
Occurs at transcription level = genes can be switched ON or OFF
= controlled gene expression

5. Operon Model A 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!

6. Operon Model A 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

7. 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

8. 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

9. Lac operon
Inducible operon (in contrast w/ trp repressor operon)

10. Promoter, repressor, operator, gene
Lac operon
“PROG”:
Promoter, repressor, operator, gene
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

11. 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

12. 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
BUT
The complexity of a euk. cell allows for controlled gene expression at many different stages
1. Target DNA – pre-transcription
2. Target RNA – post-transcription
3. Target Protein – post-translation

13. Target DNA Remember… How is DNA packaged? Let’s draw
Label: histone, DNA, nucleosome, and N-terminus tail of histone

14. Target DNA HISTONE modifications can affect gene transcription
N-terminus tail is easily accessible to modifying proteins that add or remove chemical groups

15. 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

16. 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

17. Target DNA SUMMING UP HISTONE modifications:
HISTONE ACETYLATION = loosens chromatin increase transcription of gene
B. DNA METHYLATION = blocks transcription of gene

18. 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)

19. 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

20. Target Protein
FUN FACT! In 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!