1. Regulation of Gene Expression
An In-depth Review of Chapter 18

2. “While all cells of an organism have all genes in the genome, not all genes are expressed in every cell.” “Both unicellular organisms and multicellular organisms must continually turn genes on and off in response to signals from their external and internal environments”

3. Gene Expression:
A gene (a segment of DNA) is undergoing transcription.
Transcription leads to translation, which leads to proteins.
This takes energy!
Cells don’t want to waste energy if they don’t have too! There is no need to make ‘photoreceptors’ if the cell is inside your big toe.

4. Gene Regulation How do you regulate things in the body?
“On/Off” switches: chromatin remodeling, operator
“Dimmer” switches: microRNA, RNAi

5. Feedback Mechanisms POSITIVE NEGATIVE
Final product of the reaction accelerates the pathway
Ex. Childbirth/Labor
Final product of the reaction inhibits/stops the pathway
Ex. Tryptophan Synthesis in E. coli

6. A
Negative
feedback 
Enzyme 1 B D
Enzyme 2
Excess D
blocks a step D D C
Enzyme 3 D
(a) Negative feedback W
Enzyme 4 X
Positive
feedback +
Enzyme 5
Excess Z
stimulates a
step Z Y Z Z
Enzyme 6 Z
(b) Positive feedback

7. Overview Gene Regulation
PROKARYOTE
EUKARYOTE
Simpler
Regulate at the level of transcription
lac & trp operon
Much, much, much more complex.
Regulate at any level really.
Differential gene expression leads to cell differentiation

8. Prokaryotes  E. coli
“Consider an individual E. coli cell living in the erratic environment of the human colon, dependent for its nutrients on the whimsical eating habits of the host.”
“If the environment is lacking the amino acid tryptophan (which the bacterium needs to survive), the cell responds but activating a biochemical pathway that creates it.”
“Later if the host eats a tryptophan-rich meal, the bacterial cells stops producing it (saves energy)”

9. Okay… so the E. coli can inhibit and turn on gene expression… but how?

10. Polypeptide subunits that make up enzymes for tryptophan synthesis
trp operon
Promoter
Promoter
Genes of operon
DNA
trpR
trpE
trpD
trpC
trpB
trpA
Regulatory
gene
Operator
Start codon
Stop codon 3
mRNA 5
mRNA
RNA
polymerase 5 E D C B A
Protein
Inactive
repressor
Polypeptide subunits that make up
enzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
DNA
No RNA made
mRNA
Protein
Active
repressor
Tryptophan
(corepressor)
(b) Tryptophan present, repressor active, operon off

11. Polypeptide subunits that make up enzymes for tryptophan synthesis
trp operon
Promoter
Genes of operon
trpE
trpD
trpC
trpB
trpA
Operator
Start codon
Stop codon
mRNA 5 E D C B A
Polypeptide subunits that make up
enzymes for tryptophan synthesis
Promoter: region of DNA where RNA poly binds
Operator: “on/off” switch, controls if RNA poly can bind or not. NO RNA POLY. BINDING = NO TRANSCTIPTION
Operon: Whole segment of DNA including the promoter, operator, and the genes they control.

12. Promoter: region of DNA where RNA poly binds.
Fig. 18-3a
trp operon
Promoter
Promoter
Genes of operon
DNA
trpR
trpE
trpD
Regulatory
gene
Operator
Start codon 3
mRNA 5
mRNA 5 E D
Protein
Inactive
repressor
Promoter: region of DNA where RNA poly binds.
Regulatory Gene: genes that are located away from the operon itself but control the transcription of specific genes.
Repressor: protein that binds to the operator that turns off (represses) transcription.

13. Co-repressor: smaller molecule that activates the repressor protein.
DNA
No RNA made
mRNA
Protein
Active
repressor
Tryptophan
(corepressor)
Co-repressor: smaller molecule that activates the repressor protein.
Repressible operon: pathway that is normally “on” that can be inhibited by a repressor.
Inducible operon: pathway that is normally “off” that can be turned “on” (induced).

14. trp operon OVERVIEW YES NO TRYPTOPHAN Operon is always “on”
If trp is available the cell won’t waste energy making it.
Repressor protein combines with the available trp (co-repressor) and bind to the operator which stops the transcription of the enzymes that make tryptophan.
Negative Feedback
Operon is always “on”
The cell will continue to make repressors but without trp (co-repressor) in the environment, the repressor is not active.
Cell makes enzymes that make trp for the cell.

15. Prokaryotes  E. coli
“Consider an individual E. coli cell living in the erratic environment of the human colon, dependent for its nutrients on the whimsical eating habits of the host.”
“Lactose (milk sugar) is available in the colon if the host drinks milk.”
“Bacteria break down lactose into two monosaccharides by the enzyme B-galactosidase.”
“If lactose is increased in the E. coli’s environment then the concentration of B-galactosidase increases rapidly.”

16. (a) Lactose absent, repressor active, operon off
Regulatory
gene
Promoter
Operator
DNA
lacI
lacZ No
RNA
made 3
mRNA
RNA
polymerase 5
Active
repressor
Protein
(a) Lactose absent, repressor active, operon off
lac operon
DNA
lacI
lacZ
lacY
lacA
RNA
polymerase 3
mRNA
mRNA 5 5
-Galactosidase
Permease
Protein
Transacetylase
Allolactose
(inducer)
Inactive
repressor
(b) Lactose present, repressor inactive, operon on

17. Promoter
Regulatory
gene
Operator
DNA
lacI
lacZ No
RNA
made 3
mRNA
RNA
polymerase 5
Active
repressor
Protein
NO LACTOSE IN ENVIRONMENT = repressor is active = whole operon off = no enzymes created (because none are needed)

18. lac operon
DNA
lacI
lacZ
lacY
lacA
RNA
polymerase 3
mRNA
mRNA 5 5
-Galactosidase
Permease
Transacetylase
Protein
Allolactose
(inducer)
Inactive
repressor
Inducer: smaller molecule that binds to a repressor making it inactive.
LACTOSE PRESENT IN ENVIRONMENT = inducer binds to repressor = repressor is inactivated = operon stays on & enzymes are produced to break down the lactose

19. lac operon OVERVIEW YES NO LACTOSE Operon is normally “off”
If lactose is available the cell needs enzymes to break it down.
Repressor protein combines with the available lactose (inducer) which inactivates the repressor. This allows the cell to make the enzyme.
Operon is normally “off”
Repressor is active because there is no inducer to bind to it to turn it off
no enzymes created (because none are needed)
Lac: Induces the pathway to turn on by de-activating the repressor that is turning it off.
Trp: Inhibits the pathway (turns off) by activating the repressor

20. Ok. Enough of the easy stuff. Moving on to eukaryotes…

21. Differential Gene Expression
Many different cell types.
The differences in these cell types is not because they have different DNA but rather they are expressing different genes within the same genome.
Prokaryotes regulate their genes by controlling transcription… how do eukaryotes regulate their genes?

22. Signal
All the boxes in the picture are areas where eukaryotes can regulate gene expression.
Complex.
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Protein processing
Active protein
Degradation
of protein
Transport to cellular
destination
Cellular function

23. Signal
Chromatin (chromosome) Modification:
Acetylation: loosen DNA structure  makes it easier for transcription to occur
Methylation: tightens DNA structure  makes it harder for transcription to occur
AKA:
Chromatin-modifying enzymes provide initial control of gene expression by making DNA more or less able to bind to transcription machinery.
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
mRNA in nucleus
Cap
Transport to cytoplasm
CYTOPLASM

24. Signal
Transcription:
In order for transcription to occur at all in eukaryotes, enhancers and activators interact with various transcription factors to affect gene expression.
AKA:
Complex folding and specific binding occurs for every gene that is transcribed.
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
mRNA in nucleus
Cap
Transport to cytoplasm
CYTOPLASM

25. Promoter Activators Gene DNA Enhancer
Distal control
element
Enhancer
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
Activators attach to specific DNA segments to for an enhancer region. DNA binding proteins bring the enhancer region next to the promoter. Various binding occurs allowing RNA poly. To begin transcription. (BINDING IS SPECIFIC TO EACH REACTION).
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis

26. Signal
RNA Processing:
Alternative RNA Splicing: different mRNA molecules are produced from the same primary transcript.
mRNA Lifespan longer in eukaryotes than prokaryotes.
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Tail
mRNA in nucleus
Cap
Transport to cytoplasm
CYTOPLASM

27. Exons
DNA
Troponin T gene
Primary
RNA
transcript
RNA splicing
mRNA or

28. Noncoding RNA’s Role Chromatin modification Translation
• Small RNAs can promote the formation of
heterochromatin in certain regions, blocking
transcription.
Chromatin modification
Transcription
Translation
RNA processing
• miRNA or siRNA can block the translation
of specific mRNAs.
mRNA
degradation
Translation
Protein processing
and degradation
mRNA degradation
Noncoding RNA’s Role
• miRNA or siRNA can target specific mRNAs
for destruction.

29. mRNA & proteins degrade over time
Much quicker in prokaryotes (which allows them to adapt to new situations much more rapidly than eukaryotes can)
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Protein
fragments
(peptides)
Protein entering a
proteasome

30. Overview Gene Regulation
PROKARYOTE
EUKARYOTE
Simpler
Regulate at the level of transcription
lac & trp operon
Much, much, much more complex.
Regulate at any level really.
Differential gene expression leads to cell differentiation

31. Cell Differentiation
Cells express specific genes to become specialized in structure and function

33. Embryology
Three main process that lead from a fertilized egg to a fully developed organism.
1.) Cell Division
2.) Cell Differentiation (Specialize)
3.) Morphogenesis (form/distribution)

34. Cell Division

35. Cell Differentiation
From sperm and egg… what tells each cell which gene to express at any given time in development?
1.) Cytoplasmic Determinants
2.) Inductions by nearby cells

36. Morphogenesis Spatial Organization Homeotic genes (Hox genes) Dorsal
Right
Anterior
Posterior
Left
Ventral

38. Mutated Hox Genes
Eye
Leg
Antenna
Wild type
Mutant

39. Mutated Hox Genes