AP BIO Chap 18

Overview: Conducting the Genetic

Orchestra

• Prokaryotes and eukaryotes alter gene

expression in response to their changing

environment

• In multicellular eukaryotes, gene expression

regulates development and is responsible for

differences in cell types

• RNA molecules play many roles in regulating

gene expression in eukaryotes

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Bacteria often respond to environmental

change by regulating transcription

• Natural selection has favored bacteria that

produce only the products needed by that cell

• A cell can regulate the production of enzymes by

feedback inhibition or by gene regulation

• Gene expression in bacteria is controlled by the

operon model

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Precursor

Feedbac

k

inhibition

Enzyme 1

Enzyme 2

Enzyme 3

Tryptophan

(a) Regulation of enzyme (b)

activity

Regulation of enzyme

production

Regulation

of gene

expression

−

−

trpE gene

trpD gene

trpC gene

trpB gene

trpA gene

Figure 18.2

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

• An operon is the entire stretch of DNA that

includes the operator, the promoter, and the genes

that they control

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• The operon can be switched off by a protein

repressor

• The repressor prevents gene transcription by

binding to the operator and blocking RNA

polymerase

• The repressor is the product of a separate

regulatory gene

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• The repressor can be in an active or inactive form,

depending on the presence of other molecules

• A corepressor is a molecule that cooperates with

a repressor protein to switch an operon off

• For example, E. coli can synthesize the amino

acid tryptophan

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• By default the trp operon is on and the genes for

tryptophan synthesis are transcribed

• 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

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Promoter

DNA

Regulatory

gene

mRNA

trpR

5′

3′

Protein Inactive

repressor

RNA

polymerase

Promoter

trp

operon

Genes of operon

Operator

mRNA 5′

Start codon Stop codon

trpE trpD trpC trpB trpA

E D C B A

Polypeptide subunits that make up

enzymes for tryptophan synthesis

(a) Tryptophan absent, repressor inactive, operon on

(b) Tryptophan present, repressor active, operon off

DNA

mRNA

Protein

Tryptophan

(corepressor)

Active

repressor

No RNA

made

Figure 18.3

Figure 18.3b-1

(b) Tryptophan present, repressor active, operon off

DNA

mRNA

Protein

Tryptophan

(corepressor)

Active

repressor

Figure 18.3b-2

(b) Tryptophan present, repressor active, operon off

DNA

mRNA

Protein

Tryptophan

(corepressor)

Active

repressor

No RNA

made

Figure 18.3a

Promoter

DNA

Regulatory

gene

mRNA

trpR

5′

3′

Protein Inactive

repressor

RNA

polymerase

Promoter

trp operon

Genes of operon

Operator

mRNA 5′

Start codon Stop codon

trpE trpD trpC trpB trpA

E D C B A

Polypeptide subunits that make up

enzymes for tryptophan synthesis

(a) Tryptophan absent, repressor inactive, operon on

Repressible and Inducible Operons: Two

Types of Negative Gene Regulation

• A repressible operon is one that is usually on;

binding of a repressor to the operator shuts off

transcription

• The trp operon is a repressible operon

• An inducible operon is one that is usually off; a

molecule called an inducer inactivates the

repressor and turns on transcription

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• The lac operon is an inducible operon and

contains genes that code for enzymes used in the

hydrolysis and metabolism of lactose

• By itself, the lac repressor is active and switches

the lac operon off

• A molecule called an inducer inactivates the

repressor to turn the lac operon on

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(a) Lactose absent, repressor active, operon off

(b) Lactose present, repressor inactive, operon

on

Regulatory

gene

Promoter

Operator

DNA lacI lacZ

lacI

DNA

mRNA

5′

3′

No

RNA

made

RNA

polymerase

Active

Protein repressor

lac operon

DNA lacZ lacY lacA

mRNA

5′

3′

Protein

mRNA 5′

Inactive

repressor

RNA polymerase

Allolactose

(inducer)

β-Galactosidase Permease Transacetylase

Figure 18.4

Figure 18.4a

(a) Lactose absent, repressor active, operon off

Regulatory

gene

Promoter

Operator

DNA lacI lacZ

mRNA

5′

3′

No

RNA

made

RNA

polymerase

Active

repressor Protein

Figure 18.4b

(b) Lactose present, repressor inactive, operon on

lacI

lac operon

lacZ lac

Y

lac

A

DNA

mRNA

5

′

3

′

Protein

mRNA 5′

Inactive

repressor

RNA polymerase

Allolactose

(inducer)

β-Galactosidase Permease Transacetylase

• Inducible enzymes usually function in catabolic

pathways; their synthesis is induced by a chemical

signal

• Repressible enzymes usually function in anabolic

pathways; their synthesis is repressed by high

levels of the end product

• Regulation of the trp and lac operons involves

negative control of genes because operons are

switched off by the active form of the repressor

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Positive Gene Regulation

• Some operons are also subject to positive control

through a stimulatory protein, such as catabolite

activator protein (CAP), an activator of

transcription

• When glucose (a preferred food source of E. coli)

is scarce, CAP is activated by binding with cyclic

AMP (cAMP)

• Activated CAP attaches to the promoter of the lac

operon and increases the affinity of RNA

polymerase, thus accelerating transcription

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• When glucose levels increase, CAP detaches from

the lac operon, and transcription returns to a

normal rate

• CAP helps regulate other operons that encode

enzymes used in catabolic pathways

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Figure 18.5a

Promoter

DNA

CAP-binding site

lacI lacZ

RNA

polymerase

binds and

transcribes

Operator

cAMP

Active

CAP

Inactive

CAP

Allolactose

Inactive lac

repressor

(a) Lactose present, glucose scarce (cAMP level high):

abundant lac mRNA synthesized

Figure 18.5b

Promoter

DNA

CAP-binding site

lacI lacZ

Operator

RNA

polymerase less

likely to bind

Inactive lac

repressor

Inactive

CAP

(b) Lactose present, glucose present (cAMP level low):

little lac mRNA synthesized

Figure 18.5 Promoter

DNA

CAP-binding site

lacI lacZ

RNA

polymerase

binds and

transcribes

Operator

cAMP

Active

CAP

Inactive

CAP

Allolactose

Inactive lac

repressor

(a) Lactose present, glucose scarce (cAMP level high):

abundant lac mRNA synthesized

Promoter

DNA

CAP-binding site

lacI lacZ

Operator

RNA

polymerase less

likely to bind

Inactive lac

repressor

Inactive

CAP

(b) Lactose present, glucose present (cAMP level low):

little lac mRNA synthesized

Eukaryotic gene expression is regulated at

many stages

• All organisms must regulate which genes are

expressed at any given time

• In multicellular organisms regulation of gene

expression is essential for cell specialization

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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

• Abnormalities in gene expression can lead to

diseases including cancer

• Gene expression is regulated at many stages

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Figure 18.6a Signal

NUCLEUS

Chromatin

Chromatin modification:

DNA unpacking involving

histone acetylation and

DNA demethylation

DNA

Gene

Gene available

for transcription

RNA Exo

n Primary transcript

Transcription

Intron

RNA processing

Cap

Tail

mRNA in nucleus

Transport to cytoplasm

CYTOPLASM

Figure 18.6b

CYTOPLASM

mRNA in cytoplasm

Degradation Translation

of mRNA

Polypeptide

Protein processing, such

as cleavage and

chemical modification

Active protein

Degradation

of protein

Transport to

cellular

destination

Cellular function (such

as enzymatic activity,

structural support)

Figure 18.6 Signal

NUCLEUS

Chromatin

Chromatin modification:

DNA unpacking involving

histone acetylation and

DNA demethylation

DNA

Gen

e

Gene available

for transcription

RNA Exo

n Primary transcript

Transcription

Intron

RNA processing

Cap

Tail

mRNA in nucleus

Transport to cytoplasm

CYTOPLASM

mRNA in cytoplasm

Degradation Translation

of mRNA

Polypeptide

Protein processing, such

as cleavage and

chemical modification

Active protein

Degradation

of protein

Transport to

cellular

destination

Cellular function (such

as enzymatic activity,

structural support)

Regulation of Chromatin Structure

• Genes within highly packed heterochromatin are

usually not expressed

• Chemical modifications to histones and DNA of

chromatin influence both chromatin structure and

gene expression

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Histone Modifications

• In histone acetylation, acetyl groups are

attached to positively charged lysines in histone

tails

• This loosens chromatin structure, thereby

promoting the initiation of transcription

• The addition of methyl groups (methylation) can

condense chromatin; the addition of phosphate

groups (phosphorylation) next to a methylated

amino acid can loosen chromatin

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Figure 18.7

Amino acids

available

for chemical

modification

Histone

tails

DNA

double

helix

Nucleosome

(end view)

(a) Histone tails protrude outward from a nucleosome

Unacetylated histones Acetylated histones

(b) Acetylation of histone tails promotes loose chromatin

structure that permits transcription

• The histone code hypothesis proposes that

specific combinations of modifications, as well as

the order in which they occur, help determine

chromatin configuration and influence transcription

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DNA Methylation

• DNA methylation, the addition of methyl groups

to certain bases in DNA, is associated with

reduced transcription in some species

• DNA methylation can cause long-term inactivation

of genes in cellular differentiation

• In genomic imprinting, methylation regulates

expression of either the maternal or paternal

alleles of certain genes at the start of development

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Epigenetic Inheritance

• Although the chromatin modifications just

discussed 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

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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

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Organization of a Typical Eukaryotic Gene

• Associated with most eukaryotic genes are

multiple control elements, segments of

noncoding DNA that serve as binding sites for

transcription factors that help regulate

transcription

• Control elements and the transcription factors they

bind are critical to the precise regulation of gene

expression in different cell types

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Figure 18.8-3

Enhancer

(distal control

elements)

DNA

Upstream Promoter

Proximal

control

elements

Transcription

start site

Exon Intron Exon Intron Exon

Poly-A

signal

sequence

Transcription

termination

region

Downstream Poly-A

signal

Exon Intron Exon Intron Exon

Transcription

Cleaved

3′ end of

primary

transcript

5′

Primary RNA

transcript

(pre-mRNA)

Intron

RNA

RNA processing

mRNA

Coding segment

5′ Cap 5′ UTR

Start

codon

Stop

codon 3′ UTR

3′

Poly-A

tail

G P P P AAA ⋅⋅⋅AAA

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

• In eukaryotes, high levels of transcription of

particular genes depend on control elements

interacting with specific transcription factors

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• Proximal control elements are located close to the

promoter

• Distal control elements, groupings of which are

called enhancers, may be far away from a gene

or even located in an intron

Enhancers and Specific Transcription

Factors

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• An activator is a protein that binds to an enhancer

and stimulates transcription of a gene

• Activators have two domains, one that binds DNA

and a second that activates transcription

• Bound activators facilitate a sequence of protein-

protein interactions that result in transcription of a

given gene

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Figure 18.9

DNA

Activation

domain

DNA-binding

domain

• Some transcription factors function as repressors,

inhibiting expression of a particular gene by a

variety of methods

• Some activators and repressors act indirectly by

influencing chromatin structure to promote or

silence transcription

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Activators

DNA

Enhancer Distal control

element

Promoter

Gene

TATA box

General

transcription

factors

DNA-

bending

protein

Group of mediator proteins

RNA

polymerase II

RNA

polymerase II

RNA synthesis

Transcription

initiation complex

Figure 18.10-3

Control

elements

Enhancer Promoter

Albumin gene

Crystallin

gene

LIVER

Coordinately Controlled Genes in Eukaryotes

• Unlike the genes of a prokaryotic operon, each of

the co-expressed eukaryotic genes has a

promoter and control elements

• These genes can be scattered over different

chromosomes, but each has the same

combination of control elements

• Copies of the activators recognize specific control

elements and promote simultaneous transcription

of the genes

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Nuclear Architecture and Gene Expression

• Loops of chromatin extend from individual

chromosomes into specific sites in the nucleus

• Loops from different chromosomes may

congregate at particular sites, some of which are

rich in transcription factors and RNA polymerases

• These may be areas specialized for a common

function

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Figure 18.12

Chromosome

territory

Chromosomes in the

interphase nucleus

Chromatin

loop

Transcription

factory

10 μm

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

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RNA Processing

• 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

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Exons

DNA

Troponin T gene

Primary

RNA

transcript

RNA splicing

mRNA or

1

1

1 1

2

2

2 2

3

3

3

4

4

4

5

5

5 5

Figure 18.13

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

• Nucleotide sequences that influence the lifespan

of mRNA in eukaryotes reside in the untranslated

region (UTR) at the 3′ end of the molecule

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Initiation of Translation

• The initiation of translation of selected

mRNAs can be blocked by regulatory proteins that

bind to sequences or structures of the mRNA

• Alternatively, translation of all mRNAs

in a cell may be regulated simultaneously

• For example, translation initiation factors are

simultaneously activated in an egg following

fertilization

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Protein Processing and Degradation

• After translation, various types of protein

processing, including cleavage and the addition of

chemical groups, are subject to control

• Proteasomes are giant protein complexes that

bind protein molecules and degrade them

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Figure 18.14

Protein to

be degraded

Ubiquitin

Ubiquitinate

d

protein

Proteasome

Protein entering

a proteasome

Proteasome

and ubiquitin

to be recycled

Protein

fragments

(peptides)