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Chapter 18:
Regulation of Gene Expression
AP Biology
Overview: Conducting the Genetic Orchestra
• Prokaryotes and eukaryotes alter gene expression in response to changes in
environmental conditions
– Multicellular eukaryotes must also develop and maintain multiple cell types
• Though multicellular eukaryotes have different types of cells, all of these
cells contain the same genome
– A significant challenge in the gene regulation of these organisms is
controlling the expression of different subsets of genes to create
different cell types
• Gene expression is often regulated at the stage of transcription, but control at other
levels of gene expression is also important
– RNA molecules play many roles in regulating gene expression in eukaryotes
Concept 18.1: Bacteria often respond to
environmental change by regulating transcription
Fig. 18-2
Regulationof geneexpression
trpE gene
trpD gene
trpC gene
trpB gene
trpA gene
(b) Regulation of enzymeproduction
(a) Regulation of enzymeactivity
Enzyme 1
Enzyme 2
Enzyme 3
Tryptophan
Precursor
Feedback
inhibition
Regulation of Enzyme Activity and Production
• Natural selection has favored bacteria that produce only the products needed by that
cell
– By doing so, these bacteria can conserve resources and energy for other
important tasks
• Metabolic control occurs on 2 levels:
– First, cells can adjust the activity of enzymes that are already present by
feedback inhibition
• In this type of inhibition, the
activity of an enzyme is inhibited
by a product in an anabolic
pathway
– Second, cells can adjust the
production level of certain enzymes
by regulating the expression of the
genes encoding these enzymes
• Gene expression in bacteria is
controlled by the operon model
Operons: The Basic Concept
• A cluster of functionally related genes can be under
coordinated control by a single on-off “switch”
– The regulatory “switch” is a segment of DNA called an
operator usually positioned within the promoter
• The operator controls access of RNA polymerase to the
genes
• An operon is the entire stretch of DNA that includes the
operator, the promoter, and the genes that they control
Repressors
• The operon can be switched off by a protein repressor
– The repressor prevents gene transcription by binding to the
operator and blocking RNA polymerase (no transcription)
– A repressor protein is specific for the operator of a particular
operon
– The repressor is the product of a separate regulatory gene
• Regulatory genes are expressed continuously, although at a
low rate, so that a few repressor molecules are always
present within the cell
Repressors (Continued)
• The binding of repressors to operators is reversible
• Operators can be in one of 2 states at any given time:
• One with repressor bound (“off” mode)
• One without the repressor bound (“on” mode)
• The relative duration of each state depends on the number of active
repressor molecules present
• The repressor can be in an active or inactive form, depending on the presence
of other molecules
• In its inactive form, the repressor has little affinity for its operator
• In its active form, a specific substrate binds to the repressor at an allosteric
site, triggering a change in conformation
• These types of substrates are examples of molecules called
corepressors that cooperates with a repressor protein to switch an
operon off
• Ex) E. coli can synthesize the amino acid tryptophan
Fig. 18-3a
Polypeptide subunits that make upenzymes for tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon on
DNA
mRNA 5
Protein Inactiverepressor
RNApolymerase
Regulatorygene
Promoter Promoter
trp operon
Genes of operon
Operator
Stop codonStart codon
mRNA
trpA
5
3
trpR trpE trpD trpC trpB
ABCDE
Operon “On”
• By default the trp operon is on and the genes for tryptophan
synthesis are transcribed
• Occurs when tryptophan is absent
• Repressor is inactive
Fig. 18-3b-2
(b) Tryptophan present, repressor active, operon off
Tryptophan(corepressor)
No RNA made
Activerepressor
mRNA
Protein
DNA
Operon “Off”
• When tryptophan is present, it binds to the trp repressor protein,
which turns the operon off
• The repressor is active only in the presence of its corepressor
tryptophan
• Thus the trp operon is turned off (repressed) if tryptophan levels
are high
Repressible and Inducible Operons: Two Types of Negative Gene Regulation
• There are 2 types of negative gene regulation:
– 1) A repressible operon is one that is usually on
• Binding of a repressor to the operator shuts off transcription
– Ex) trp operon
– 2) An inducible operon is one that is usually off
• A molecule called an inducer inactivates the repressor and turns
on transcription
– Ex) lac operon
The lac Operon: An Inducible Operon
• The lac operon is an inducible operon found in E.coli cells
– This operon contains genes that code for enzymes used in the hydrolysis and
metabolism of lactose
• Lactose metabolism begins with the hydrolysis of lactose into its
component monosaccharides – glucose and galactose
– This reaction is catalyzed by the enzyme β- galactosidase
– The gene for β-galactosidase is one of the 3 genes that code for
enzymes that function in lactose utilization
• The entire transcription unit is under the command of a single operator and
promoter
• A regulatory gene located outside the operon called lacI codes for an
allosteric repressor protein that can switch the operon “off” by binding to
the operator
Fig. 18-4b
(b) Lactose present, repressor inactive, operon on
mRNA
Protein
DNA
mRNA 5
Inactiverepressor
Allolactose(inducer)
5
3
RNApolymerase
Permease Transacetylase
lac operon
-Galactosidase
lacYlacZ lacAlacI
The lac Operon: Allolactose as an Inducer
• A molecule called an inducer inactivates the repressor to turn the lac operon on
– For the lac operon, the inducer is an isomer of lactose called allolactose
• Allolactose is formed in small amounts from lactose that enters the cell
– Allolactose binds to the lac repressor and alters its shape, preventing the
repressor from binding to the operator
• Without a bound repressor, the lac operon is transcribed into mRNA, and
the proteins needed for lactose utilization are produced
Fig. 18-4a
(a) Lactose absent, repressor active, operon off
DNA
ProteinActiverepressor
RNApolymerase
Regulatory
genePromoter
Operator
mRNA5
3
NoRNAmade
lacI lacZ
The lac Operon: Lactose Absent
• By itself, the lac repressor is active and switches the lac operon off
– Occurs due to the absence of lactose (and hence allolactose)
Inducible vs. Repressible Enzymes
• The enzymes of the lactose pathway are referred to as inducible enzymes because
their synthesis is induced by a chemical signal (allolactose)
– Inducible enzymes usually function in catabolic pathways
• The enzymes for tryptophan synthesis are referred to as repressible enzymes
because their synthesis is repressed by high levels of the end product
– Repressible enzymes usually function in anabolic pathways
• Regulation of both the trp and lac operons involves negative control of genes
because operons are switched off by the active form of the repressor
– Gene regulation is said to be positive only when a regulatory protein interacts
directly with the genome to switch transcription on
Positive Gene Regulation
• An example of positive gene regulation also involves the lac operon
– When glucose and lactose are both present, E.coli preferentially use glucose,
since the enzymes for glycolysis are always present
• E.coli use lactose as an energy source only when glucose is in short
supply
– When glucose is scarce, a small organic molecule called cyclic AMP (cAMP)
accumulates
• In this case, the lac operon is subject to positive control through a
stimulatory protein called catabolite activator protein (CAP), an activator
of transcription
• CAP is activated by binding
with cAMP, which allows it to
attach to a specific site at the
upstream end of the lac promoter
• This attachment increases the
affinity of RNA polymerase for the
promoter, thus accelerating
transcription
• When glucose levels in the cell increase, cAMP concentration decreases
– Without cAMP, CAP detaches from the lac operon
– Because CAP is inactive, the affinity of RNA polymerase for the promoter of the
lac operon is lowered
– Transcription of the lac operon will
thus proceed only at a low level, even
in the presence of lactose
• Therefore, the lac operon is under dual control:
– Negative control by the lac repressor
(like on-off switch)
• The state of the lac repressor (with or without bound allolactose)
determines whether transcription of the lac operon’s genes will occur at all
– Positive control by CAP (like volume control)
• The state of CAP (with or without bound cAMP) controls the rate of
transcription if the operon is repressor-free
• CAP also helps regulate other operons that encode enzymes used in catabolic
pathways
Dual Control of the lac Operon
Concept 18.2: Eukaryotic gene expression can be
regulated at any stage
Gene Expression and Cell Specialization
• All organisms must regulate which genes are expressed at any
given time
– In multicellular organisms gene expression is essential for
cell specialization
• To perform its role, each cell type must maintain a
specific program of gene expression in which certain
genes are expressed and others are not
Differential Gene Expression
• Almost all the cells in an organism are genetically identical
– Differences between cell types result from differential gene
expression, the expression of different genes by cells with the same
genome
• A typical human cell expresses only ~20% of its genes at any given
time
– Errors in gene expression can lead to diseases including cancer
• Gene expression in eukaryotic cells is regulated at many stages
– Each stage is a potential control point at which gene expression can be
turned on or off, accelerated, or slowed down
Regulation of Gene Expression at Transcription
• In all organisms, a common control point for gene expression is at
transcription
– Regulation at this stage is often in response to signals
(hormones, signaling molecules) coming from outside the cell
– For this reason, the term “gene expression” is often equated with
transcription for both bacteria and eukaryotes
• The greater complexity of eukaryotes, however, also
provides opportunities for regulating gene expression at
many additional stages
Fig. 18-6
DNA
Signal
Gene
NUCLEUS
Chromatin modification
Chromatin
Gene available
for transcription
Exon
Intron
Tail
RNA
Cap
RNA processing
Primary transcript
mRNA in nucleus
Transport to cytoplasm
mRNA in cytoplasm
Translation
CYTOPLASM
Degradation
of mRNA
Protein processing
Polypeptide
Active protein
Cellular function
Transport to cellular
destination
Degradation
of protein
Transcription
• In this diagram, the colored boxes indicate
processes most often regulated
– Each color indicates the type of
molecule affected (blue=DNA,
orange=RNA, purple=protein)
– The nuclear envelope separating
transcription and translation in
eukaryotic cells offers opportunities
for post-transcriptional control in the
form of RNA processing
– In addition, eukaryotes have a greater
variety of control mechanisms
operating before transcription and
after translation
Regulation of Chromatin Structure
• The structural organization of chromatin not only packs a cell’s DNA
into a compact form that fits inside the nucleus, but it also helps
regulate gene expression in several ways
– The location of a gene’s promoter can affect whether a gene will
be transcribed
– In addition, genes within highly packed heterochromatin are
usually not expressed
– Chemical modifications to histones and DNA of chromatin also
influence both chromatin structure and gene expression
Fig. 18-7
Histonetails
DNA
double helix
(a) Histone tails protrude outward from anucleosome
Acetylated histones
Aminoacidsavailablefor chemicalmodification
(b) Acetylation of histone tails promotes loosechromatin structure that permits transcription
Unacetylated histones
Histone Modifications
• There is mounting evidence that chemical modifications to histones play a
direct role in regulation of gene transcription
– The N-terminus of each histone molecule protrudes outward from the
nucleosome
– These histone tails are
accessible to various
modifying enzymes that
catalyze the addition or
removal of specific
chemical groups
Fig. 18-7
Histonetails
DNA
double helix
(a) Histone tails protrude outward from anucleosome
Acetylated histones
Aminoacidsavailablefor chemicalmodification
(b) Acetylation of histone tails promotes loosechromatin structure that permits transcription
Unacetylated histones
Histone Acetylation
• In histone acetylation, acetyl groups (-COCH3) are attached to positively
charged lysines in histone tails
– When lysines are acetylated, their positive charges are neutralized
• As a result, histone tails no longer bind to neighboring
nucleosomes
– This process loosens chromatin structure and allows transcription
proteins easier access to
genes, thereby promoting
the initiation of
transcription
Other Histone Modifications
• Several other chemical groups can be reversibly attached to amino acids in
histone tails, including methyl and phosphate groups
– The addition of methyl groups (methylation) can condense chromatin
– The addition of phosphate groups (phosphorylation) next to a methylated
amino acid can loosen chromatin
• The discovery that these and other modifications to histone tails can affect
chromatin structure and gene expression has led to the histone code hypothesis
– This hypothesis proposes that specific combinations of modifications,
rather than the overall level of histone acetylation, help determine
chromatin configuration
• Chromatin configuration, in turn, has a direct influence on transcription
DNA Methylation
• Some enzymes can methylate certain bases of DNA itself
– DNA methylation, the addition of methyl groups to certain bases in DNA, is
associated with reduced transcription in some species
• Ex) The inactivated mammalian X chromosome is generally more
methylated than DNA that is actively transcribed
– DNA methylation can also cause long-term inactivation of genes in cellular
differentiation
• Methylation patterns are passed on to successive generations of cells, so
that cells keep a chemical record of what occurred during embryonic
development
• A methylation pattern maintained in this way accounts for genomic
imprinting in mammals
– In genomic imprinting, methylation regulates expression of either the
maternal or paternal alleles of certain genes at the start of
development
Epigenetic Inheritance
• Although chromatin modifications do not alter DNA sequence,
they may be passed to future generations of cells
– The inheritance of traits transmitted by mechanisms not
directly involving the nucleotide sequence is called
epigenetic inheritance
• Epigenetic variations might help explain why one
identical twin acquires a genetically based disease
(schizophrenia), but the other does not, despite their
identical genomes
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
– Once the chromatin of a gene is optimally modified for expression, the
initiation of transcription is the next major step at which gene
expression is regulated
• Involves proteins that bind to DNA and either facilitate or inhibit
binding of RNA polymerase (transcription factors)
• Before looking at how eukaryotic cells control transcription,
however, it is helpful to review the structure of a typical eukaryotic
gene
Fig. 18-8-3
Enhancer
(distal control elements)Proximal
control elements
Poly-A signalsequence
Terminationregion
DownstreamPromoter
UpstreamDNA
ExonExon ExonIntron Intron
Exon Exon ExonIntronIntronCleaved 3 endof primarytranscript
Primary RNAtranscript
Poly-Asignal
Transcription
5
RNA processing
Intron RNA
Coding segment
mRNA
5 Cap 5 UTRStart
codonStop
codon 3 UTR Poly-A
tail
3
• In a typical eukaryotic gene, a cluster of proteins called a transcription initiation
complex assembles on the promoter sequence at the “upstream” end of a gene
– One of these proteins (RNA polymerase II) then proceeds to transcribe the
gene, producing a primary RNA transcript
• RNA processing follows, including enzymatic addition of a 5’ cap and a
poly-A tail, as well as splicing out of introns
– Associated with most eukaryotic genes are control elements, segments of
noncoding DNA that help regulate transcription by binding certain proteins
• Control elements and the proteins they bind are critical to the precise
regulation of gene expression in different cell types
The Roles of Transcription Factors
• To initiate transcription, eukaryotic RNA polymerase requires the assistance of
proteins called transcription factors
– General transcription factors are essential for the transcription of all protein-
coding genes
• Most of these transcription factors do not bind DNA directly, but bind to
proteins (including each other) and RNA polymerase II
• These protein-protein interactions are crucial to the initiation of eukaryotic
transcription
• The interactions of general transcription factors and RNA polymerase II
with a promoter, however, usually only lead to a low rate of transcription
– In eukaryotes, high levels of transcription of particular genes depend on control
elements interacting with another set of proteins called specific transcription
factors
Proximal vs. Distal Control Elements
• Some of these specific transcription factors are called proximal control
elements because they are located close to the promoter
• More distant groups of specific transcription factors called enhancers may
be located 1000s of nucleotides upstream or downstream of a gene, or even
within an intron
– These enhancers are referred to as distal control elements
• A given gene may have multiple enhancers, each active at a
different time or in a different cell type or location within an
organism
• Each enhancer, however, is only associated with one specific gene
Activators and Mediator Proteins
• In eukaryotes, the rate of gene expression can be strongly controlled by the binding
of special proteins to the control elements of enhancers
– An activator is a protein that binds to an enhancer and stimulates transcription
of a gene
• Protein-mediated bending of DNA is thought to bring bound activators in
contact with another group of proteins called mediator proteins
– These mediator proteins will, in turn, interact with proteins at the
promoter
• These multiple protein-protein interactions help assemble and position the
initiation complex on the promoter
Animation: Initiation of Transcription
Fig. 18-9-3
Enhancer TATAbox
PromoterActivators
DNAGene
Distal controlelement
Group ofmediator proteins
DNA-bending
protein
Generaltranscriptionfactors
RNApolymerase II
RNApolymerase II
Transcriptioninitiation complex RNA synthesis
• Step 1: Activator proteins bind to distal control elements grouped as an enhancer in
the DNA
– This particular enhancer has 3 binding sites
• Step 2: A DNA-bending protein brings the bound activator closer to the promoter
– General transcription
factors, mediator
proteins, and RNA
polymerase are
nearby
• Step 3: The activator bind
to certain mediator proteins
and general transcription
factors, helping them form
an active transcription
initiation complex on
the promoter
• Some transcription factors function as repressors, inhibiting expression of a
particular gene
– Some repressors bind directly to control element DNA, like enhancers
• This may block activator binding or turn off transcription even when
activators are bound
– Other repressors block the binding of activators to proteins that allow activators
to bind to DNA
• Some activators and repressors act indirectly by influencing chromatin structure to
promote or silence transcription
– Activators may recruit proteins that acetylate histones near the promoters of
specific genes, thereby promoting transcription
– Some repressors recruit proteins that deacetylate histones, leading to reduced
transcription
Coordinately Controlled Genes in Eukaryotes
• In bacteria, coordinately controlled genes are often clustered in an operon that is
regulated by a single promoter and transcribed in a single mRNA molecule
– In eukaryotic cells, some co-expressed genes are also clustered near one
another of the same chromosomes, but each has its own promoter and control
elements
– More commonly, however, these genes are scattered over different
chromosomes, but each has the same combination of control elements
• Copies of the activators recognize these specific control elements and
promote simultaneous transcription of the genes, no matter where they are
in a genome
– This coordinated control often occurs in response to chemical signals
(ex: hormones) from outside the cell
• These signals bind to receptor proteins, forming complexes that
serves as transcription activators
– Every gene whose transcription is stimulated by a particular chemical
signal has a control element recognized by the same complex,
regardless of its chromosomal location
Mechanisms of Post-Transcriptional Regulation
• Transcription alone does not account for gene
expression
– Regulatory mechanisms can operate at various
stages after transcription
– Such mechanisms allow a cell to fine-tune gene
expression rapidly in response to environmental
changes
Fig. 18-11
or
RNA splicing
mRNA
PrimaryRNAtranscript
Troponin T gene
Exons
DNA
RNA Processing
• RNA processing in the nucleus and export of mature RNA to the cytoplasm provide
several opportunities for regulating gene expression in eukaryotic cells
– 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
• Regulatory proteins specific to each cell type control intron-exon choices
by binding to regulatory sequences
in the primary transcript
– Ex) The troponin T gene
encodes 2 different
proteins
mRNA Degradation
• The life span of mRNA molecules in the cytoplasm is a key to determining
protein synthesis
– Eukaryotic mRNA is more long lived than prokaryotic mRNA, allowing
them to be translated repeatedly in these cells
– The mRNA life span is determined in part by sequences in the leader
and trailer regions
• Nucleotide sequences that affect how long an mRNA remains
intact are often found in the untranslated region (UTR) at the 3’ end
Animation: mRNA Degradation
Initiation of Translation
• Translation presents another opportunity for regulating gene expression
– Occurs most commonly at the initiation stage
• The initiation of translation of some mRNAs can be blocked by regulatory
proteins that bind to sequences or structures within the 5’ UTR of the
mRNA
– This prevents attachment of ribosomes and hence translation
• Alternatively, translation of all mRNAs
in a cell may be regulated simultaneously
– Usually involves activation or inactivation of one or more protein
factors required to initiate translation
• Ex) Translation initiation factors are simultaneously
activated in an egg following fertilization
Animation: Blocking Translation
Protein Processing and Degradation
• The final opportunity for controlling gene expression occurs after translation
– Eukaryotic polypeptides must often be processed to yield functional protein
molecules
• These various types of protein processing include cleavage and chemical
modifications
– Ex) Regulatory proteins are commonly activated or inactivated by the
reversible addition of phosphate groups
– The length of time each protein functions in a cell is also strictly regulated by
means of selective degradation
• To mark a particular protein for destruction, the cell often attaches
molecules of a small protein called ubiquitin to that protein
• Giant protein complexes called proteasomes recognize these ubiquitin-
tagged proteins and degrade them
Animation: Protein Degradation Animation: Protein Processing
Degradation of a Protein by a Proteasome
• Step 1: Multiple ubiquitin molecules are attached to a protein by enzymes in
the cytosol
• Step 2: The ubiquitin-tagged protein is recognized by a proteasome , which
unfolds the protein and sequesters it within a central cavity
• Step 3: Enzymatic components of the proteasome cut the protein into small
peptides, which can be further degraded by other enzymes in the cytosol
Fig. 18-12
Proteasomeand ubiquitinto be recycledProteasome
Proteinfragments(peptides)Protein entering a
proteasome
Ubiquitinatedprotein
Protein tobe degraded
Ubiquitin
Concept 18.3: Noncoding RNAs play multiple roles
in controlling gene expression
Noncoding RNAs and Regulation of Gene Expression
• Only a small fraction (1.5% in humans) of DNA codes for
proteins, rRNA, and tRNA
– A significant amount of the genome may be transcribed into
noncoding RNAs
• Noncoding RNAs regulate gene expression at two
points:
– mRNA translation
– Chromatin configuration
Effects on mRNAs by MicroRNAs and Small Interfering RNAs
• MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to
complementary sequences of mRNA
– miRNAs are formed from longer RNA precursors that fold back on themselves,
forming one or more double-stranded hairpin structures, each held together by
hydrogen bonds
– After each hairpin is cut away from the precursor, it is trimmed by an enzyme
called a Dicer into a short, double-stranded fragment of ~20 nucleotide pairs
– One of the two strands is degraded, while the other strand (the miRNA) forms a
complex with one or more proteins
• The miRNA allows this complex to bind to any mRNA molecule with a
complementary sequence
• The miRNA-protein complex then either degrades the target mRNA or
blocks its translation
– The expression of an estimated 1/3 of all human genes may be
regulated by miRNAs
Fig. 18-13
miRNA-proteincomplex(a) Primary miRNA transcript
Translation blocked
Hydrogenbond
(b) Generation and function of miRNAs
Hairpin miRNA
miRNA
Dicer
3
mRNA degraded
5
• Step 1: An enzyme cuts each hairpin from the primary miRNA transcript
• Step 2: A second enzyme called Dicer trims the loop and the single-stranded ends
from the hairpin (cuts are made at the arrows)
• Step 3: One strand of the double-stranded RNA is degraded
– The other strand (miRNA) than forms a complex with one or more proteins
• Step 4: The miRNA in the complex can bind to any target mRNA that contains at
least 6 bases of complementary
sequence
• Step 5: If miRNA and mRNA
bases are complementary all
along their length, the
mRNA is degraded (left)
– If the match is less
complete, translation
is blocked (right)
Small Interfering RNAs
• Gene expression can also be blocked by RNA molecules called small
interfering RNAs (siRNAs)
– The phenomenon of inhibition of gene expression by RNA molecules is
called RNA interference (RNAi)
• siRNAs and miRNAs are similar but form from different RNA
precursors
– miRNA is formed from a single hairpin in a precursor RNA
– siRNAs are formed from much longer double-stranded RNA
molecules, each which gives rise to many siRNAs
Chromatin Remodeling and Silencing of Transcription by Small RNAs
• Small RNA molecules can also cause remodeling of chromatin structure
– siRNAs play a role in heterochromatin formation and can block large
regions of the chromosome
• An RNA transcript produced from DNA is copied into double-
stranded RNA, which is then processed into several siRNAs
• These siRNAs associate with a complex of proteins, which then
recruit enzymes that modify the chromatin, turning it into the highly
condensed heterochromatin
– Small RNAs may also block transcription of specific genes
Concept 18.4: A program of differential gene
expression leads to the different cell types in a multicellular organism
A program of differential gene expression leads to the different cell types in a multicellular organism
• During embryonic development, a fertilized egg gives rise to
many different cell types
– Cell types are organized successively into tissues, organs,
organ systems, and the whole organism
• Gene expression orchestrates this developmental
program, producing cells of different types that form
these higher-level structures
• The transformation from zygote to adult results from 3 interrelated processes:
– Cell division
• The zygote gives rise to a large number of cells through a succession of
mitotic cell division
– Cell differentiation
• These daughter cells then become specialized in structure and function
– Morphogenesis
• These different types of
cells are organized into
tissues and organs in a
particular 3-dimensional
arrangement that give an
organism its shape
Fig. 18-14
(a) Fertilized eggs of a frog (b) Newly hatched tadpole
A Genetic Program for Embryonic Development
• Differential gene expression results from genes being
regulated differently in each cell type
– Materials placed into an egg by the mother set up
a sequential program of gene regulation that is
carried out as cells divide
– This program makes the cells become different
from each other in a coordinated fashion
Fig. 18-15a
(a) Cytoplasmic determinants in the egg
Two differentcytoplasmicdeterminants
Unfertilized egg cell
Sperm
Fertilization
Zygote
Mitoticcell division
Two-celledembryo
Nucleus
Cytoplasmic Determinants and Inductive Signals
• Two sources of information “tell” a cell which genes to express at any given time
during embryonic development
– An egg’s cytoplasm contains RNA, proteins, and other substances that are
distributed unevenly in the unfertilized egg
• These substances include
cytoplasmic determinants,
maternal substances in the
egg that influence early development
– As the zygote divides by mitosis,
cells contain different cytoplasmic
determinants, which lead to
different gene expression
Fig. 18-15b
(b) Induction by nearby cells
Signalmolecule(inducer)
Signaltransductionpathway
Early embryo(32 cells)
NUCLEUS
Signalreceptor
Induction
• The other important source of developmental information is the environment around
the cell, especially signals from nearby embryonic cells
– In the process called induction, signal molecules from embryonic cells cause
transcriptional changes in nearby target cells
• Gene expression is therefore altered in these cells
• Thus, interactions between cells
induce differentiation of
specialized cell types
Animation: Cell Signaling
Sequential Regulation of Gene Expression During Cellular Differentiation
• The term determination refers to the events that lead to the observable
differentiation of a cell
– Once a cell has undergone determination, it is irreversibly committed to its final
fate
• If a committed cell is experimentally placed in another location in the
embryo, it will still differentiate into the cell type that is its normal fate
• Determination precedes differentiation
– Observable cellular differentiation is marked by the expression of genes for
tissue-specific proteins
• These proteins are found only in a specific cell type and give the cell its
characteristic structure and function
Differentiation of Skeletal Muscle Cells
• We can look at the differentiation of skeletal muscle cells as an example:
– Muscle cells develop from embryonic precursor cells that have the potential to
develop into a number of cell types, including cartilage and fat cells
– Once determination occurs, these cells are called myoblasts
• Myoblasts produce muscle-specific proteins and eventually differentiate to
form skeletal muscle cells
– MyoD is one of several “master regulatory genes” that produce proteins that
commit the cell to becoming skeletal muscle
• This gene encodes MyoD protein, a transcription factor that binds to
enhancers of various target genes and stimulates their expression
• Then, secondary transcription factors activate the genes for proteins such
as myosin and actin that confer the unique properties of skeletal muscle
cells
Fig. 18-16-3
Embryonicprecursor cell
Nucleus
OFF
DNA
Master regulatory gene myoD Other muscle-specific genes
OFF
OFFmRNA
MyoD protein(transcriptionfactor)
Myoblast(determined)
mRNA mRNA mRNA mRNA
Myosin, othermuscle proteins,and cell cycle–blocking proteinsPart of a muscle fiber
(fully differentiated cell)
MyoD Anothertranscriptionfactor
• Step 1: Determination - Signals from other cells lead to activation of the master
regulatory gene myoD, allowing the cell to make MyoD protein, which acts as an
activator
– The cell is now called a myoblast and is irreversibly committed to becoming a
skeletal muscle cell
• Step 2: Differentiation - MyoD protein stimulates the myoD gene further and
activates genes encoding for other muscle-specific transcription factors
– These transcription factors
activate genes for muscle
proteins like myosin and actin
– MyoD also turns on
genes that block the
cell cycle, thus
stopping cell division
– The nondividing
myoblasts fuse to
become mature
multinucleate muscle
cells, also called
muscle fibers
Pattern Formation: Setting Up the Body Plan
• For differentiated cells and tissues to function effectively in the organism as a whole,
the organism’s body plan (its 3-D arrangement) must be established and
superimposed on the differentiation process
– Pattern formation is the development of a spatial organization of tissues and
organs
• In animals, pattern formation begins with the establishment of the major
axes
– The three major axes of a bilaterally symmetrical animal include head
and tail, right and left sides, and back and front
• The molecular cues that control pattern formation are collectively known as
positional information
– These cytoplasmic determinants and inductive signals tell a cell its
location relative to the body axes and to neighboring cells
Pattern Formation in Drosophila
• Pattern formation has been extensively studied in
the fruit fly Drosophila melanogaster
– Combining anatomical, genetic, and
biochemical approaches, researchers have
discovered developmental principles common
to many other species, including humans
The Life Cycle of Drosophila
• In Drosophila, cytoplasmic determinants in the unfertilized egg provide
positional information for the placement of anterior-posterior and dorsal-
ventral axes even before fertilization
– This egg develops in the female’s ovary, surrounded by ovarian cells
called nurse cells and follicle cells
• These support cells supply the egg with nutrients, mRNAs, and
other substances needed for development and make the egg shell
• After fertilization, the embryo develops into a segmented larva with
three larval stages
Fig. 18-17bFollicle cell
Nucleus
Eggcell
Nurse cell
Egg celldeveloping withinovarian follicle
Unfertilized egg
Fertilized egg
Depletednurse cells
Eggshell
FertilizationLaying of egg
Bodysegments
Embryonicdevelopment
Hatching
0.1 mm
Segmentedembryo
Larval stage
(b) Development from egg to larva
1
2
3
4
5
• 1) The yellow egg is surrounded by other cells that form a structure called the follicle
within one of the mother’s ovaries
• 2)Nurse cells shrink as they supply nutrients and mRNAs to the developing egg,
which grows larger
– Eventually, the mature egg fills
the egg shell that is secreted by
the follicle cells
• 3)The egg is fertilized within the
mother and then laid
• 4-5) Embryonic development forms
a larva that goes through 3 stages
– The 3rd stage forms a cocoon (not shown), within
which the larva metamorphoses into the
adult shown
Fig. 18-18
Antenna
MutantWild type
Eye
Leg
Genetic Analysis of Early Development: Scientific Inquiry
• Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel
1995 Prize for decoding pattern formation in Drosophila
– These scientists studied mutant flies with developmental defects that led to
extra wings or legs in the wrong places
• They located these mutations on the fly’s genetic map, thus connecting
developmental abnormalities to specific genes
– Their research supplied the first concrete evidence that genes somehow direct
developmental processes
• These genes that
control pattern
formation in the late
embryo, larva, and
adult are called
homeotic genes
• Thirty years later, Nüsslein-Volhard and Wieschaus set out to identify all the
genes that affect segment formation in Drosophila
– They created mutants, conducted breeding experiments, and looked for
corresponding genes
• Breeding experiments were complicated by embryonic lethals,
embryos with lethal mutations
– They found 120 genes essential for normal segmentation
• The researchers were able to group these segmentation genes by
general function, to map them, and to clone many of them for
further study in the lab
Axis Establishment
• Maternal effect genes encode for cytoplasmic determinants that initially establish
the axes of the body of Drosophila
– When these genes are mutant in the mother, any offspring display the mutant
phenotype regardless of the offspring’s own genotype
– These maternal effect genes are also called egg-polarity genes because they
control orientation of the egg and consequently, that of the fly
• One group of these genes sets up the anterior-posterior axis of the
embryo, while a second group establishes the dorsal-ventral axis
– Mutations in these maternal effect genes are generally embryonic lethals
Animation: Development of Head-Tail Axis in Fruit Flies
Fig. 18-19a
T1 T2T3
A1 A2 A3 A4 A5 A6A7
A8
A8
A7 A6 A7
Tail
TailTail
Head
Wild-type larva
Mutant larva (bicoid)
EXPERIMENT
A8
The Bicoid Gene
• One maternal effect gene, the bicoid gene, affects the front half of the body
– An embryo whose mother has a mutant bicoid gene lacks the front half of its
body and has duplicate posterior structures at both ends
• This phenotype suggested that the product of the mother’s bicoid gene is
essential for setting up the anterior end of the fly and therefore might be
concentrated at the future anterior end of the embryo
• This hypothesis is an example of the
morphogen gradient hypothesis, in
which gradients of substances called
morphogens establish an embryo’s axes
and other features of its form
Fig. 18-19b
Fertilization,
translation
of bicoid
mRNA Bicoid protein in earlyembryo
Anterior end
Bicoid mRNA in matureunfertilized egg
100 µm
RESULTS
• Experiment: many embryos and larvae with defects in their body patterns were
obtained
– Some of these defects were due to mutations in the mother’s genes, including
the bicoid (“two-tailed”) gene, which resulted in larvae with two tails and no
head
– The researchers hypothesized that bicoid normally codes for a morphogen
specifying the head (anterior) end of the embryo
• To test this hypothesis, they used molecular techniques to determine
where the mRNA and protein encoded by this gene were found in the
fertilized egg and early embryo
• Results: bicoid mRNA (dark blue) was confined to the anterior end of the
unfertilized egg
– Later in development, Bicoid protein was seen to be concentrated in cells at the
anterior end of the embryo
• Conclusion: the results support the hypothesis that Bicoid protein is a morphogen
specifying formation of head-
specific structures
Importance of Bicoid Research • The bicoid research is important for three reasons:
– It identified a specific protein required for some early steps in pattern formation
• This helped us understand how different regions of the egg can give rise to
cells that go down different developmental pathways
– It increased understanding of the mother’s role in embryo development
– It demonstrated the key developmental principle that a gradient of molecules
can determine polarity and position in the embryo
• In Drosophila, gradients of specific proteins determine the posterior and
anterior ends, as well as the dorsal-ventral axis
• Positional information later establishes a specific number of correctly
oriented segments and triggers the formation of each segment’s
characteristic structures
– The pattern of the adult is abnormal when the genes operating in this
final step are abnormal
Concept 18.5: Cancer results from genetic changes
that affect cell cycle control
Cancer and Gene Regulation
• The gene regulation systems that go wrong during cancer are the very same
systems involved in embryonic development
– Cancer can be caused by mutations to genes that regulate cell growth
and division
• The agents of these changes can be random spontaneous
mutation, or they may be caused by environmental influences,
including chemical carcinogens and X-rays
• Tumor viruses can also cause cancer in animals, including
humans
– Ex) Human papillomaviruses (HPV) are associated with
cervical cancer
Oncogenes and Proto-Oncogenes
• Oncogenes are cancer-causing genes
– Proto-oncogenes are the corresponding normal cellular
genes that are responsible for normal cell growth and
division
• An oncogene usually arises from a genetic change that
leads to an increase either in the amount of the gene’s
protein product or in the activity of each protein
molecule
– Conversion of a proto-oncogene to an oncogene can
lead to abnormal stimulation of the cell cycle
Conversion of Proto-Oncogenes to Oncogenes
• Genetic changes that convert proto-oncogenes to oncogenes fall into 3 main
categories:
– Movement of DNA (translocation) within the genome: if it ends up near an
active promoter, transcription may increase
– Amplification of a proto-oncogene: increases the number of copies of the proto-
oncogene in the cell
– Point mutation in a control element or in the proto-oncogene itself, causing an
increase in gene expression
Fig. 18-20
Normal growth-stimulatingprotein in excess
Newpromoter
DNA
Proto-oncogene
Gene amplification:Translocation ortransposition:
Normal growth-stimulatingprotein in excess
Normal growth-stimulatingprotein in excess
Hyperactive ordegradation-resistant protein
Point mutation:
Oncogene Oncogene
within a control element within the gene
Tumor-Suppressor Genes
• Cells also contain genes known as tumor-suppressor genes whose normal
products inhibit cell division
– The proteins they encode help prevent uncontrolled cell growth
– Mutations that decrease protein products of tumor-suppressor genes may
contribute to cancer onset
• The protein products of tumor-suppressor genes have various functions:
– Repair damaged DNA, preventing the cell from accumulating cancer-causing
mutations
– Control adhesion of cells to one another or to the extracellular matrix, which is
crucial in normal tissues and often absent in cancers
– Inhibit the cell cycle in the cell-signaling pathway
Interference with Normal Cell-Signaling Pathways
• The proteins encoded by many proto-oncogenes and tumor-
suppressor genes are components of cell-signaling pathways
– The products of 2 key genes, ras proto-oncogene and the
p53 tumor-suppressor gene, can be examined in order to
elucidate what goes wrong with the functioning of these
proteins in cancer cells
• Mutations in the ras gene can lead to production of a
hyperactive Ras protein and increased cell division
The Ras Protein
• The Ras (named for rat sarcoma) protein is a G protein that relays a signal
from a growth factor receptor on the plasma membrane to a cascade of
protein kinases
– The cellular response at the end of the pathway is the synthesis of a
protein that stimulates the cell cycle
• Normally, this pathway will not operate unless triggered by the
appropriate growth factor
• Certain mutations in the ras gene can lead to production of a
hyperactive Ras protein that triggers the kinase cascade even in
the absence of growth factor
– Results in increased cell division
Fig. 18-21a
Receptor
Growthfactor
G protein GTP
Ras
GTP
Ras
Protein kinases(phosphorylationcascade)
Transcriptionfactor (activator)
DNA
HyperactiveRas protein(product ofoncogene)issuessignalson its own
MUTATION
NUCLEUS
Gene expression
Protein thatstimulatesthe cell cycle
(a) Cell cycle–stimulating pathway
11
3
4
5
2
• The normal cell cycle-stimulating pathway is triggered by a growth factor (1) that
binds to its receptor (2) in the plasma membrane
• The signal is relayed to a G protein (3) called Ras
– Ras is active when GTP is bound to it
• Ras passes the signal to a series of protein kinases (4)
• The last kinase (5) activates a
transcription activator that turns on
one or more genes for proteins that
stimulate the cell cycle
– Results in excessive
cell division that may
cause cancer
The p53 Gene • If the DNA of a cell is damaged, another signaling pathway blocks the cell cycle until
the damage has been repaired
– Thus, the genes for components of this pathway act as tumor-suppressor
genes
• One is these genes, called the p53 gene, encodes a specific transcription
factor that promotes the synthesis of cell cycle-inhibiting proteins
– Activates a gene called p21 whose product halts the cell cycle by
binding to cyclin-dependent kinases, thus allowing time for DNA repair
– Also turns on genes directly involved in DNA repair
– When DNA damage is irreparable, p53 activates “suicide genes”
whose proteins cause cell death by apoptosis
• A mutation that knocks out the p53 gene can lead to excessive cell growth
and cancer
• In the normal cell cycle-inhibiting pathway, DNA damage (1) is an
intracellular signal that is passed via protein kinases (2) and leads to
activation of p53 (3)
– Activated p53 promotes transcription of the gene for a protein that
inhibits the cell cycle
• This suppression ensures that damaged DNA is not replicated Fig. 18-21b
MUTATION
Protein kinases
DNA
DNA damagein genome
Defective or
missing
transcription
factor, such
as p53, cannot
activate
transcription
Protein that
inhibits
the cell cycle
Activeformof p53
UVlight
(b) Cell cycle–inhibiting pathway
2
3
1
Fig. 18-21
Receptor
Growth
factor
G protein
GTP
Ras
GTP
Ras
Protein kinases
(phosphorylation
cascade)
Transcription
factor (activator)
DNA
Hyperactive
Ras protein
(product of
oncogene)
issues
signals
on its own
MUTATION
NUCLEUS
Gene expression
Protein that
stimulates
the cell cycle
(a) Cell cycle–stimulating pathway
MUTATION
Protein kinases
DNA
DNA damage
in genome
Defective or
missing
transcription
factor, such
as p53, cannot
activate
transcription
Protein that
inhibits
the cell cycle
Active
form
of p53
UV
light
(b) Cell cycle–inhibiting pathway
(c) Effects of mutations
EFFECTS OF MUTATIONS
Cell cycle not
inhibited
Protein absent
Increased cell
division
Protein
overexpressed
Cell cycle
overstimulated
1
2
3
4
5
2
1
3
• Mutations causing deficiencies in
any pathway component can
contribute to the development
of cancer
– Increased cell division that
may lead to cancer can
result if the cell cycle is
over-stimulated via the
cell cycle-stimulating
pathway (a)
– A similar effect can be seen
if the mutation affects the
cell cycle-inhibiting
pathway (b)
The Multistep Model of Cancer Development
• Multiple mutations are generally needed for full-fledged cancer
– The longer we live, the more mutations we accumulate
• This may help explain why the incidence of cancer
increases greatly with age
– At the DNA level, a cancerous cell is usually characterized
by at least one active oncogene and the mutation of
several tumor-suppressor genes
• The model of a multistep path to cancer is well-supported by studies of colorectal
cancer
– Like most cancers, colorectal cancer develops gradually
• The 1st sign is often a polyp, made up of cells that look normal but divide
unusually frequently
• The tumor grows and may eventually become malignant, spreading to
other tissues
– The development of this malignant tumor is caused by a gradual accumulation
of mutations that convert proto-oncogenes to oncogenes and knock out tumor-
suppressor genes
• A ras oncogene and a mutated p53 tumor-suppressor gene are often
involved
Fig. 18-22
EFFECTS OF MUTATIONS
Malignant tumor
(carcinoma)
Colon
Colon wall
Loss of tumor-
suppressor gene
APC (or other)
Activation of
ras oncogene
Loss of
tumor-suppressor
gene DCC
Loss of
tumor-suppressor
gene p53
Additional
mutations
Larger benign
growth (adenoma)
Small benign
growth (polyp)
Normal colon
epithelial cells
5
42
3
1
Inherited Predisposition and Other Factors Contributing to Cancer
• Individuals can inherit oncogenes or mutant alleles of
tumor-suppressor genes
– Inherited mutations in the tumor-suppressor gene
adenomatous polyposis coli are common in
individuals with colorectal cancer
– Mutations in the BRCA1 or BRCA2 gene are found
in at least half of inherited breast cancers
You should now be able to:
1. Explain the concept of an operon and the
function of the operator, repressor, and
corepressor
2. Explain the adaptive advantage of grouping
bacterial genes into an operon
3. Explain how repressible and inducible operons
differ and how those differences reflect
differences in the pathways they control
4. Explain how DNA methylation and histone
acetylation affect chromatin structure and the
regulation of transcription
5. Define control elements and explain how they
influence transcription
6. Explain the role of promoters, enhancers,
activators, and repressors in transcription
control
7. Explain how eukaryotic genes can be
coordinately expressed
8. Describe the roles played by small RNAs on
gene expression
9. Explain why determination precedes
differentiation
10. Describe two sources of information that
instruct a cell to express genes at the
appropriate time
11. Explain how maternal effect genes affect polarity and development in Drosophila embryos
12. Explain how mutations in tumor-suppressor genes can contribute to cancer
13. Describe the effects of mutations to the p53 and ras genes