1. How are genes turned on & off?
E. coli, a type of bacteria that lives in the human colon
Can tune its metabolism to the changing environment and food sources

2. This metabolic control occurs on two levels
Adjusting the activity of metabolic enzymes already present
Regulating the genes encoding the metabolic enzymes
Figure 18.20a, b
(a) Regulation of enzyme activity
Enzyme 1
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
Regulation
of gene
expression
Feedback
inhibition
Tryptophan
Precursor
(b) Regulation of enzyme production
Gene 2
Gene 1
Gene 3
Gene 4
Gene 5 –

3. Operons: The Basic Concept
In bacteria, genes are often clustered into operons, composed of
An operator, an “on-off” switch
A promoter
Genes for metabolic enzymes

4. An operon
Is usually turned “on”
Can be switched off by a protein called a repressor

5. The trp operon: regulated synthesis of repressible enzymes
Figure 18.21a
(a) Tryptophan absent, repressor inactive, operon on. RNA polymerase attaches to the DNA at the promoter and transcribes the operon’s genes.
Genes of operon
Inactive repressor
Protein
Operator
Polypeptides that make up
enzymes for tryptophan synthesis
Promoter
Regulatory
gene
RNA polymerase
Start codon Stop codon
trp operon 5 3
mRNA 5
trpD
trpE
trpC
trpB
trpA
trpR
DNA
mRNA E D C B A

6. Tryptophan present, repressor active, operon off. As tryptophan
DNA
mRNA
Protein
Tryptophan
(corepressor)
Active
repressor
No RNA made
Tryptophan present, repressor active, operon off. As tryptophan
accumulates, it inhibits its own production by activating the repressor protein.
(b)
Figure 18.21b

7. Repressible and Inducible Operons: Two Types of Negative Gene Regulation
In a repressible operon
Binding of a specific repressor protein to the operator shuts off transcription
In an inducible operon
Binding of an inducer to an innately inactive repressor inactivates the repressor and turns on transcription

8. The lac operon: regulated synthesis of inducible enzymes
Figure 18.22a
DNA
mRNA
Protein
Active repressor
RNA polymerase
No RNA made
lacZ
lacl
Regulatory gene
Operator
Promoter
Lactose absent, repressor active, operon off. The lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator.
(a) 5 3

9. lacl mRNA 5' DNA mRNA Protein Allolactose (inducer) Inactive repressor
lacz
lacY
lacA
RNA polymerase
Permease
Transacetylase
-Galactosidase 5 3
(b)
Lactose present, repressor inactive, operon on. Allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor. In this way, the enzymes for lactose utilization are induced.
mRNA 5
lac operon
Figure 18.22b

10. Inducible enzymes Repressible enzymes
Usually function in catabolic pathways
Repressible enzymes
Usually function in anabolic pathways

11. Regulation of both the trp and lac operons
Involves the negative control of genes, because the operons are switched off by the active form of the repressor protein

12. Positive Gene Regulation
Some operons are also subject to positive control
Via a stimulatory activator protein, such as catabolite activator protein (CAP)

13. In E. coli, when glucose, a preferred food source, is scarce
The lac operon is activated by the binding of a regulatory protein, catabolite activator protein (CAP)
Promoter
Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for the lactose pathway.
(a)
CAP-binding site
Operator
RNA
polymerase
can bind and transcribe
Inactive CAP
Active CAP
cAMP
DNA
Inactive lac
repressor
lacl
lacZ
Figure 18.23a

14. When glucose levels in an E. coli cell increase
CAP detaches from the lac operon, turning it off
Figure 18.23b
(b)
Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription.
Inactive lac
repressor
Inactive CAP
DNA
RNA
polymerase
can’t bind
Operator
lacl
lacZ
CAP-binding site
Promoter

15. Eukaryotic Gene Regulation

16. In eukaryotes, the DNA-protein complex, called chromatin is ordered into higher structural levels than the DNA-protein complex in prokaryotes
Figure 19.1

17. Both prokaryotes and eukaryotes
Must alter their patterns of gene expression in response to changes in environmental conditions
Eukaryotic DNA
Is precisely combined with a large amount of protein
Eukaryotic chromosomes
Contain an enormous amount of DNA relative to their condensed length

18. Nucleosomes, or “Beads on a String”
Proteins called histones
Are responsible for the first level of DNA packing in chromatin
Bind tightly to DNA
The association of DNA and histones
Seems to remain intact throughout the cell cycle

19. (a) Nucleosomes (10-nm fiber)
In electron micrographs
Unfolded chromatin has the appearance of beads on a string
Each “bead” is a nucleosome
The basic unit of DNA packing
2 nm
10 nm
DNA double helix
Histone
tails
His-
tones
Linker DNA
(“string”)
Nucleosome
(“bad”)
Histone H1
(a) Nucleosomes (10-nm fiber)
Figure 19.2 a

20. Gene expression can be regulated at any stage, but the key step is transcription
All organisms must regulate which genes are expressed at any given time
During development of a multicellular organism its cells undergo a process of specialization in form and function called cell differentiation

21. Differential Gene Expression
Each cell of a multicellular eukaryote expresses only a fraction of its genes
In each type of differentiated cell, a unique subset of genes is expressed
Many key stages of gene expression can be regulated in eukaryotic cells
Genes within highly packed chromatin are usually not expressed
Figure 19.3
Signal
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethlation
Gene
DNA
Gene available
for transcription
RNA
Exon
Transcription
Primary transcript
RNA processing
Transport to cytoplasm
Intron
Cap
mRNA in nucleus
Tail
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypetide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein

22. Regulation of Transcription Initiation
Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery (how tightly packed is the chromatin?)

23. Organization of a Typical Eukaryotic Gene
Associated with most eukaryotic genes are multiple control elements
Segments of noncoding DNA that help regulate transcription by binding certain proteins
Enhancer
(distal control elements)
Proximal
control elements
DNA
Upstream
Promoter
Exon
Intron
Poly-A signal
sequence
Termination
region
Transcription
Downstream
Poly-A
signal
Primary RNA
transcript
(pre-mRNA) 5
Intron RNA
RNA processing:
Cap and tail added;
introns excised and
exons spliced together
Coding segment P G
mRNA
5 Cap
5 UTR
(untranslated
region)
Start
codon
Stop
3 UTR
tail
Chromatin changes
RNA processing
degradation
Translation
Protein processing
and degradation
Cleared 3 end
of primary
transport
Figure 19.5

24. The Roles of Transcription Factors
To initiate transcription
Eukaryotic RNA polymerase requires the assistance of proteins called transcription factors
*Enhancers and Specific Transcription Factors:
Proximal control elements
Are located close to the promoter
Distal control elements, groups of which are called enhancers
May be far away from a gene or even in an intron

25. An activator
Is a protein that binds to an enhancer and stimulates transcription of a gene
Distal control
element
Activators
Enhancer
Promoter
Gene
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
Mediator proteins
RNA
Polymerase II
RNA synthesis
Transcription
Initiation complex
Chromatin changes
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
A DNA-bending protein
brings the bound activators
closer to the promoter.
Other transcription factors,
mediator proteins, and RNA
polymerase are nearby. 2
Activator proteins bind
to distal control elements
grouped as an enhancer in
the DNA. This enhancer has
three binding sites. 1
The activators bind to
certain general transcription
factors and mediator
proteins, helping them form
an active transcription
initiation complex on the promoter. 3
Figure 19.6

26. Some specific transcription factors function as repressors to inhibit expression of a particular gene
Some activators and repressors act indirectly by influencing chromatin structure

27. Coordinately Controlled Genes
Unlike the genes of a prokaryotic operon
Coordinately controlled eukaryotic genes each have a promoter and control elements
The same regulatory sequences
Are common to all the genes of a group, enabling recognition by the same specific transcription factors

28. Mechanisms of Post-Transcriptional Regulation
An increasing number of examples are being found of regulatory mechanisms that operate at various stages after transcription
In alternative RNA splicing different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns
Chromatin changes
Transcription
RNA processing
mRNA
degradation
Translation
Protein processing
and degradation
Exons
DNA
Primary
RNA
transcript
RNA splicing or

29. mRNA Degradation
The life span of mRNA molecules in the cytoplasm is an important factor in determining the protein synthesis in a cell &is determined in part by sequences in the leader and trailer regions
What happens if genes involved in regulating the cell cycle are turned on/off at the wrong times?