Transcript Chapter 5 Gases - Annmarie Kotarba | Nurse, Teacher and

Eldra Solomon
Linda Berg
Diana W. Martin
www.cengage.com/biology/solomon
Chapter 14
Gene Regulation
Albia Dugger • Miami Dade College
Gene Regulation
• Cells differ because gene expression is regulated, and only
certain subsets of the total genetic information are expressed
in any given cell
• Gene expression involves three basic steps, each of which is
regulated in many ways:
• Transcribing the gene to form messenger RNA (mRNA)
• Translating mRNA into protein
• Activating the protein
Control Mechanisms
• Mechanisms that regulate gene expression include:
• control of the amount of mRNA transcribed
• rate of translation of mRNA
• activity of the protein product
• Control mechanisms use various signals, some originating
within the cell and others coming from other cells or from the
environment
14.1 GENE REGULATION IN
BACTERIA AND EUKARYOTES
LEARNING OBJECTIVE:
• Explain why bacterial and eukaryotic cells have different
mechanisms of gene regulation
Bacterial Gene Regulation
• The main requirement of bacterial gene regulation is
production of enzymes and other proteins when needed
• Transcriptional-level control is the most efficient
mechanism – bacteria rarely regulate enzyme levels by
degrading proteins
• Related genes are organized into groups that are rapidly
turned on and off as units
Eukaryotic Gene Regulation
• Because a single gene is regulated in different ways in
different types of cells, eukaryotic gene regulation is complex
• Transcriptional-level control predominates, but control at other
levels of gene expression is also very important, especially in
multicellular organisms
• In many instances, pre-formed enzymes and other proteins
are rapidly converted from an inactive to an active state
• In multicellular organisms, each type of cell has certain genes
that are active and other genes that may never be used
KEY CONCEPTS 14.1
• Cells regulate which genes will be expressed and when
• Gene regulation in bacteria is primarily in response to stimuli
in the environment; gene regulation in eukaryotes helps to
maintain homeostasis
14.2 GENE REGULATION
IN BACTERIA
LEARNING OBJECTIVES:
• Define operon and explain the functions of the operator and
promoter regions
• Distinguish among inducible, repressible, and constitutive
genes
• Differentiate between positive and negative control, and show
how both types of control operate in regulating the lac operon
• Describe the types of posttranscriptional control in bacteria
Bacterial Gene Expression
• The E. coli bacterium has some genes that encode proteins
that are always needed (constitutive genes), and some that
encode proteins that are needed only in certain conditions
• Example:
• E. coli living in the colon of a calf need enzymes that
digest the milk sugar lactose
• E. coli living in the colon of an adult cow are not exposed
to milk and do not need lactose-digesting enzymes
Enzyme Activity
• Cell metabolic activity is controlled in two ways:
• By regulating the activity of certain enzymes (how
effectively an enzyme molecule works)
• By regulating the number of enzyme molecules present in
each cell
• Bacteria respond rapidly to changing environmental
conditions because functionally related genes are regulated
together in gene complexes called operons
Operons in Bacteria
• The DNA coding sequences for all three enzymes needed to
digest lactose are linked as a unit on bacterial DNA and are
controlled by a common mechanism
• Each enzyme-coding sequence is a structural gene
• operon
• A gene complex consisting of a group of structural genes
with related functions plus the closely linked DNA
sequences responsible for controlling them
The lac Operon
• The structural genes of the lactose operon (lac operon)—
lacZ, lacY, and lacA—code for three enzymes
• RNA polymerase binds to a promoter region upstream from
the coding sequences
• A single mRNA molecule is transcribed that contains the
coding information for all three enzymes
• mRNA synthesis is controlled by a single molecular “switch,”
the operator
The lac Operator
• The operator is a sequence of bases upstream from the first
structural gene in the operon
• In the absence of lactose, a repressor protein (lactose
repressor) binds tightly to the operator
• RNA polymerase binds to the promoter but is blocked from
transcribing the protein-coding genes of the lac operon
The Lactose Repressor
• Lactose repressor protein is encoded by a repressor gene
located upstream from the promoter site
• The repressor gene is a structural gene that is constitutively
expressed (constantly transcribed)
• In the absence of lactose, the repressor protein binds
specifically to the lac operator sequence, and transcription of
the lac operon is suppressed
Turing On Transcription
• Lactose “turns on” (induces ) transcription of the lac operon
• The lactose repressor protein contains a second functional
region (an allosteric site) separate from its DNA-binding site
• In the presence of lactose, the allosteric site binds to the
inducer (allolactose) which inactivates the repressor protein
• RNA polymerase is able to actively transcribes the structural
genes of the operon
The lac Operon
lac operon
Repressor
gene
Promoter
Operator
lacZ
lacY
lacA
DNA
Transcription
Repressor
protein
mRNA
Precursor of
repressor protein
Ribosome
Translation
(a) Lactose absent. In the absence of lactose, a repressor protein, encoded
by an adjacent gene, binds to a region known as the operator, thereby
blocking transcription of the structural genes.
Fig. 14-2a, p. 310
lac operon
Repressor
gene
Promoter
Operator
lacZ
lacY
lacA
DNA
Transcription
Repressor
protein
mRNA
Precursor of
repressor protein
Ribosome
Translation
(a) Lactose absent. In the absence of lactose, a repressor protein, encoded
by an adjacent gene, binds to a region known as the operator, thereby
blocking transcription of the structural genes.
Stepped Art
Fig. 14-2a, p. 310
lac operon
Repressor
gene
mRNA
Promoter OperatorlacZ lacY lacA
RNA
polymerase
Transcription
mRNA
Inducer
(allolactose)
Repressor
protein
(inactive)
Translation
Transacetylase
Lactose permease
β -galactosidase
Enzymes for lactose metabolism
(b) Lactose present. When lactose is present, it is converted to allolactose, which
binds to the repressor at an allosteric site, altering the structure of the protein so it
no longer binds to the operator. As a result, RNA polymerase is able to transcribe
the structural genes.
Fig. 14-2b, p. 310
lac operon
Repressor
gene
mRNA
Promoter Operator lacZ lacY lacA
RNA
polymerase
Transcription
mRNA
Inducer
(allolactose)
Repressor
protein
(inactive)
Translation
Transacetylase
Lactose permease
β -galactosidase
Enzymes for lactose metabolism
(b) Lactose present. When lactose is present, it is converted to allolactose, which
binds to the repressor at an allosteric site, altering the structure of the protein so
it no longer binds to the operator. As a result, RNA polymerase is able to
Stepped Art
transcribe the structural genes.
Fig. 14-2b, p. 310
Inducible Genes
• The lac operon an inducible operon
• A repressor usually controls an inducible gene or operon
by keeping it “turned off ”
• The presence of an inducer inactivates the repressor,
permitting the gene or operon to be transcribed
• Inducible genes or operons usually code for enzymes that
break down molecules (catabolic reactions)
• This saves the energy cost of making enzymes when no
substrates are available
Repressible Genes
• Repressible operons and genes are usually “turned on” –
they are turned off only under certain conditions
• Repressible genes usually code for enzymes that synthesize
essential biological molecules from simpler materials
(anabolic reactions)
• The molecular signal for regulating these genes usually is the
end product of the anabolic pathway
The trp Operon
• The tryptophan operon (trp operon) is an example of a
repressible system
• A repressor gene codes for a repressor protein which is
synthesized in an inactive form (it can’t bind to the operator
region of the trp operon)
• When tryptophan binds to the repressor, the repressor is able
to binds to the operator, which switches the operon off –
transcription is blocked
The trp Operon
Repressor
gene
trp operon
Promoter Operator
trpE trpD
trpC trpB trpA
DNA
mRNA
RNA
polymerase
Transcription
mRNA
Translation
Repressor
protein
(inactive)
Enzymes of the tryptophan
biosynthetic pathway
Tryptophan
(a) Low intracellular tryptophan levels. Repressor protein is unable to
prevent transcription because it cannot bind to the operator.
Fig. 14-4a, p. 312
trp operon
Repressor
gene
DNA
Promoter Operator
trpE trpD
trpC trpB
trpA
Active repressor –
corepressor complex
mRNA
Inactive
repressor protein
Tryptophan
(corepressor)
(b) High intracellular tryptophan levels. The amino acid tryptophan binds to
an allosteric site on the repressor protein, changing its conformation. The
resulting active form of the repressor binds to the operator region, blocking
transcription of the operon until tryptophan is again required by the cell.
Fig. 14-4b, p. 312
Negative Regulators
and Positive Regulators
• The lac and trp operons are examples of negative control, a
regulatory mechanism in which the DNA binding regulatory
protein is a repressor that turns off transcription of the gene
• Positive control is regulation by activator proteins that bind
to DNA and thereby stimulate the transcription of a gene
• The lac operon is controlled by both a negative regulator (the
lactose repressor) and a positively acting activator protein
Positive Control of the lac Operon
• A DNA sequence near the promoter binds another regulatory
protein, the catabolite activator protein (CAP)
• When activated, CAP stimulates transcription of the lac
operon and several other bacterial operons
• In its active form, CAP is bound by an allosteric site to cyclic
AMP (cAMP)
• cAMP levels increase as cells become depleted of glucose
Positive Control (cont.)
• Activated CAP binds to the CAP binding site near the lac
operon promoter
• Binding strengthens the affinity of the promoter region for
RNA polymerase – so the rate of transcriptional initiation
accelerates in the presence of lactose
• The lac operon is fully active only if lactose is available and
intracellular glucose levels are low
Positive Control of the lac Operon
Promoter
Repressor
gene
RNA
CAP- polymerase –
binding binding
site
site
Operator lacZ lacY lacA
DNA
mRNA
RNA polymerase
binds poorly
CAP
(inactive)
Allolactose
Repressor
protein (inactive)
(a) Lactose high, glucose high, cAMP low. When glucose levels are high,
cAMP is low. CAP is in an inactive form and cannot stimulate
transcription. Transcription occurs at a low level or not at all.
Fig. 14-5a, p. 313
Promoter
Repressor
gene
RNA
CAP- polymerase –
binding binding
site
site
Operator lacZ lacY lacA
DNA
mRNA
RNA polymerase
binds poorly
CAP
(inactive)
Allolactose
Repressor
protein (inactive)
(a) Lactose high, glucose high, cAMP low. When glucose levels are high,
cAMP is low. CAP is in an inactive form and cannot stimulate
Stepped Art
transcription. Transcription occurs at a low level or not at all.
Fig. 14-5a, p. 313
Promoter
Repressor
gene
RNA
polymerase –
binding
CAPsite
binding site
Operator
DNA
lacZ
lacY lacA
RNA polymerase Transcription
binds efficiently
mRNA
mRNA
CAP
cAMP
Allolactose
Repressor protein
(inactive)
Translation
Galactoside
transacetylase
Lactose
permease
β -galactosidase
Enzymes for lactose metabolism
(b) Lactose high, glucose low, cAMP high. When glucose concentrations are low,
each CAP polypeptide has cAMP bound to its allosteric site. The active form of CAP
binds to the DNA sequence, and transcription becomes activated.
Fig. 14-5b, p. 313
Promoter
Repressor
gene
RNA
polymerase –
binding
CAPsite
binding site
Operator
DNA
lacZ
lacY lacA
RNA polymerase Transcription
binds efficiently
mRNA
mRNA
CAP
cAMP
Allolactose
Repressor protein
(inactive)
Translation
Galactoside
transacetylase
Lactose
permease
β -galactosidase
Enzymes for lactose metabolism
(b) Lactose high, glucose low, cAMP high. When glucose concentrations are
low, each CAP polypeptide has cAMP bound to its allosteric site. The active
form of CAP binds to the DNA sequence, and transcription becomes activated.
Stepped Art
Fig. 14-5b, p. 313
Binding of CAP to DNA
Transcriptional Control in Bacteria
Table 14-1, p. 314
Transcription of Constitutive Genes
• Constitutive genes are continuously transcribed, but not all
are transcribed at the same rate
• Promoter elements control transcription rate
• “Strong” promoters bind RNA polymerase more frequently
and transcribe more mRNA molecules than those with “weak”
promoters
Posttranscriptional Regulation
in Bacteria
• Posttranscriptional controls are regulatory mechanisms
that occur after transcription
• Translational controls regulate the rate at which an mRNA
molecule is translated
• Posttranslational controls act as switches that activate or
inactivate one or more existing enzymes
• Example: feedback inhibition
KEY CONCEPTS 14.2
• Gene regulation in bacteria occurs primarily at the level of
transcription; regulation of transcription can be either positive
or negative
14.3 GENE REGULATION
IN EUKARYOTIC CELLS
LEARNING OBJECTIVES:
• Discuss the structure of a typical eukaryotic gene and the DNA
elements involved in regulating that gene
• Give examples of some of the ways eukaryotic DNA-binding
proteins bind to DNA
• Illustrate how a change in chromosome structure may affect
the activity of a gene
• Explain how a gene in a multicellular organism may produce
different products in different types of cells
• Identify some of the types of regulatory controls that operate
in eukaryotes after mature mRNA is formed
Gene Regulation in Eukaryotes
• Eukaryotes have transcriptional, posttranscriptional,
translational, and posttranslational gene controls that allow
individual cells, tissues, and organs to function
• Eukaryotic genes are not typically arranged in operon-like
clusters – each eukaryotic gene has specific regulatory
sequences that control transcription
• Some genes are constitutive, others are inducible
Inducible Genes
• Some inducible genes respond to environmental threats such
as heavy-metal ingestion, viral infection, and heat shock
• Example: Some heat-shock proteins are molecular
chaperones that help proteins fold into their proper shape
• Some genes are inducible only during certain periods in the
life of the organism (controlled by temporal regulation)
• Some genes are under tissue-specific regulation
Chromosome Organization
• Chromosome organization affects expression of some genes
• In multicellular eukaryotes, only a subset of genes in any
specific type of cell is active – in many cases, inactivated
genes are irreversibly dormant
• Some inactive genes lie in highly compacted
heterochromatin, such as the inactive X chromosomes in
female mammals (Barr body)
Chromosome Organization (cont.)
• Active genes are associated with euchromatin, which is
loosely packed and allows interaction with transcription
factors and other regulatory proteins
• Chromatin can be changed between heterochromatin and
euchromatin by chemically modifying histones, the proteins
that associate with DNA to form nucleosomes
Regulation of Chromatin
Gene Inactivation by DNA Methylation
• Once a gene has been turned off by some other means, DNA
methylation ensures it will remain inactive
• Enzymes add methyl groups to certain cytosine nucleotides in
DNA, which blocks transcription
• DNA methylation can be maintained for multiple generations,
as in genomic imprinting (parental imprinting), in which
expression of certain genes is determined by whether the
allele is inherited from the female or the male parent
Genomic Imprinting and Epigenetics
• Methylation provides a mechanism for epigenetic
inheritance (changes in how a gene is expressed)
• New phenotypic traits can arise from epigenetic changes
despite the fact that the nucleotide sequence of the gene itself
has not changed
• Tumor suppressor genes that inhibit cell division (and cancer)
are sometimes inactivated epigenetically, resulting in cancer
Epigenetic Variation in the agouti Gene
Fig. 14-9, p. 316
Increasing the Number of
Copies of a Gene
• A single gene may not provide enough copies of its mRNA to
meet the cell’s needs
• Genes required only by a small group of cells may be
selectively replicated by gene amplification
Drosophila chorion gene
Gene amplification by
repeated DNA replication
of chorion gene region
Chorion gene in ovarian cell
Fig. 14-10, p. 317
Functional Promoter Elements
• Transcription requires a base pair where transcription begins
(transcription initiation site or start site) plus a sequence of
bases to which RNA polymerase binds (promoter)
• Certain promoter elements have regulatory functions and
facilitate expression of the gene – mutations in these
elements reduce the rate of transcription
• Example: The TATA box, located about 25 to 30 base pairs
upstream from the transcription initiation site
Enhancers and Silencers
• Enhancers and silencers regulate a gene on the same DNA
molecule from very long distances
• enhancers
• DNA sequences that help form an active transcription
initiation complex
• silencers
• DNA sequences that can decrease transcription
Elements That Regulate Transcription
• Eukaryotic regulatory elements include the promoter and
various enhancers and silencers
DNA
Upstream
double
helix
Silencer
TATA
box
Enhancer
Promoter
Downstream
Gene
Fig. 14-11, p. 317
Transcription Factors
• Many DNA-binding proteins that regulate transcription
(transcription factors) have been identified in humans
• Each eukaryotic transcription factor has a DNA-binding
domain plus at least one other domain that is either an
activator or a repressor of transcription for a given gene
Transcription Factors (cont.)
• Transcription in eukaryotes requires multiple regulatory
proteins that are bound to different parts of the promoter
• The general transcriptional machinery binds to the TATA box
of the promoter, and is required for RNA polymerase to bind
• An activator has at least two functional domains:
• A DNA recognition site that binds to an enhancer
• An activation site that contacts the target in the general
transcriptional machinery
Stimulation of Transcription
by an Enhancer
Enhancer
Target
proteins
RNA
polymerase
TATA box
DNA
(a) Low rate of transcription. This gene is transcribed at a basic
level when the general transcriptional machinery, including
RNA polymerase, is bound to the promoter.
Fig. 14-13a, p. 319
Enhancer
DNA
TATA box
Activator
(transcription factor)
(b) High rate of transcription. A transcription factor that functions as an
activator binds to an enhancer. The intervening DNA forms a loop,
allowing the transcription factor to contact one or more target proteins
in the general transcriptional machinery, thereby increasing the rate of
transcription. This diagram is highly simplified, and many more target
proteins than the two shown are involved.
Fig. 14-13b, p. 319
Posttranscriptional Control
• Eukaryotic mRNA molecules are capped, polyadenylated
(addition of a poly-A tail), spliced, and then transported from
the nucleus to the cytoplasm to initiate translation
• Each of these events represent potential control points
• Example: When the short poly-A tail of an mRNA is
elongated, mRNA becomes activated and is translated
Pre-mRNA Processing
• Alternative splicing patterns allow the same gene to
produce one type of protein in one tissue and a different type
of protein in another tissue
• Typically, such a gene includes at least one segment that can
be either an intron or an exon
Alternative Splicing
Exon
Potential splice sites
Exon
or intron
Intron
Exon
pre-mRNA
Alternative
splicing
Exon
Exon
Exon
Functional mRNA in
tissue A
Exon
Exon
Functional mRNA in
tissue B
Fig. 14-14, p. 319
Stability of mRNA Molecules
• Controlling the lifespan of an mRNA molecule regulates the
number of protein molecules translated from it
• In some cases, mRNA stability is under hormonal control
Posttranslational
Chemical Modifications
• Another way to control gene expression is by regulating the
activity of the gene product
• In proteolytic processing, proteins are synthesized as
inactive precursors, which are converted to an active form by
removal of a portion of the polypeptide chain
• Chemical modification (adding or removing functional
groups) reversibly alters the activity of an enzyme
- Enzymes that add phosphate groups are called
kinases; those that remove them are phosphatases
Posttranslational
Chemical Modifications (cont.)
• Posttranslational control of gene expression can also involve
protein degradation
• Proteins that are selectively targeted for degradation in a
proteasome are covalently bonded to ubiquitin
• Proteasomes are large macromolecular structures that
recognize ubiquitin tags
• Proteases (protein-degrading enzymes) associated with
proteasomes hydrolyze peptide bonds
Protein
Degradation
• As protein is
degraded, ubiquitin
molecules are
released intact and
reused
Gene Regulation in Eukaryotic Cells
Cytosol
Nucleus
Regulation of chromatin
DNA must be unpacked;
heterochroma- tin cannot be
transcribed.
Methylated DNA is inaccessible to
transcription machinery;
demethylated DNA can be
transcribed.
Regulation of transcription
Selective transcription: promoter
and enhancer elements in DNA
interact with protein transcription
factors to activate or repress
transcription.
Regulation of mRNA processing
Control mechanisms, such as rate
of intron/exon splicing, regulate
mRNA processing.
Alternative splicing of exons
produces different proteins from
same mRNA.
Regulation of mRNA transport
Controlling access to, or efficiency
of, transport through nuclear pores
regulates mRNA transport from
nucleus to cytosol.
Nuclear
pore
Regulation of translation
Translational controls determine
how often and how long specific
mRNA is translated.
Modifications to protein
Chemical modifications, such
as phosphorylation, affect
activity of protein after it is
produced.
Degradation of mRNA
Translational controls determine
degree to which mRNA is
protected from destruction;
proteins that bind to mRNA in
cytosol affect stability.
Degradation of protein
Selective degradation targets
specific proteins for
destruction by proteasomes.
Fig. 14-7, p. 315
KEY CONCEPTS 14.3
• Gene regulation in eukaryotes occurs at the levels of
transcription, posttranscription, translation, and
posttranslation