Regulation of Gene Expression Chapter 18

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Regulation of Gene ExpressionChapter 18
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Gene expression

• Flow of genetic information
• Genotype to phenotype
• Genes to proteins
• Proteins not made at random
• Specific purposes
• Appropriate times

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Control of gene expression

• Selective expression of genes
• All genes are not expressed at the same time
• Expressed at different times

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Prokaryote regulation
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Control of gene expression

• Regulate at transcription
• Gene expression responds to
• Environmental conditions
• Type of nutrients
• Amounts of nutrients
• Rapid turn over of proteins

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Fig. 18-2
Precursor
Feedback inhibition
trpE gene
Enzyme 1
trpD gene
Regulation of gene expression
trpC gene
Enzyme 2
trpB gene
Enzyme 3
trpA gene
Tryptophan
(b) Regulation of enzyme production
(a) Regulation of enzyme activity
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Prokaryote

• Anabolism
• Building up of a substance
• Catabolism
• Breaking apart a substance

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Prokaryote

• Operon
• Section of DNA
• Enzyme-coding genes
• Promoter
• Operator
• Sequence of nucleotides
• Overlaps promoter site
• Controls RNA polymerase access to the promoter

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Prokaryote

• Multiple genes are expressed in a single gene
  expression
• trp operon
• Trytophan
• Synthesis
• Lac operon
• Lactose
• Degradation

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Prokaryote

• trp Operon
• Control system to make tryptophan
• Several genes that make tryptophan
• Regulatory region

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Fig. 18-3a
trp operon
Promoter
Genes of operon
trpD
trpA
trpE
trpC
trpB
Operator
Stop codon
Start codon
mRNA 5?
RNA polymerase
mRNA
5?
A
B
C
D
E
Polypeptide subunits that make up enzymes for
tryptophan synthesis
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Prokaryote

• ?tryptophan present
• Bacteria will not make tryptophan
• Genes are not transcribed
• Enzymes will not be made
• Repression

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Prokaryote

• Repressors
• Proteins
• Bind regulatory sites (operator)
• Prevent RNA polymerase attaching to promoter
• Prevent or decrease the initiation of
  transcription

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Prokaryote

• Repressors
• Allosteric proteins
• Changes shape
• Active or inactive

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Prokaryote

• ?tryptophan
• Tryptophan binds the trp repressor
• Repressor changes shape
• Active shape
• Repressor fits DNA better
• Stops transcription
• Tryptophan is a corepressor

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Fig. 18-3b-2
DNA
No RNA made
mRNA
Protein
Active repressor
Tryptophan (corepressor)
(b) Tryptophan present, repressor active, operon
off
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Prokaryote

• ?tryptophan
• Nothing binds the repressor
• Inactive shape
• RNA polymerase can transcribe

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Fig. 18-3a
trp operon
Promoter
Promoter
Genes of operon
DNA
trpD
trpA
trpR
trpE
trpC
trpB
Operator
Regulatory gene
Stop codon
Start codon
3?
mRNA 5?
RNA polymerase
mRNA
5?
A
B
C
D
E
Protein
Inactive repressor
Polypeptide subunits that make up enzymes for
tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon
on
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Prokaryote

• Lactose
• Sugar used for energy
• Enzymes needed to break it down
• Lactose present
• Enzymes are synthesized
• Induced

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Prokaryote

• lac Operon
• Promoter
• Operator
• Genes to code for enzymes
• Metabolize (break down) lactose

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Prokaryote

• Lactose is present
• Repressor released
• Genes expressed
• Lactose absent
• Repressor binds DNA
• Stops transcription

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Prokaryote

• Allolactose
• Binds repressor
• Repressor releases from DNA
• Inducer
• Transcription begins
• Lactose levels fall
• Allolactose released from repressor
• Repressor binds DNA blocks transcription

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Fig. 18-4b
lac operon
DNA
lacY
lacZ
lacA
lacI
RNA polymerase
3?
mRNA
mRNA 5?
5?
Permease
Transacetylase
?-Galactosidase
Protein
Inactive repressor
Allolactose (inducer)
(b) Lactose present, repressor inactive, operon on
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Fig. 18-4a
Regulatory gene
Promoter
Operator
DNA
lacI
lacZ
No RNA made
3?
mRNA
RNA polymerase
5?
Active repressor
Protein
(a) Lactose absent, repressor active, operon off
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Prokaryote

• Lactose tryptophan metabolism
• Adjustment by bacteria
• Regulates protein synthesis
• Response to environment
• Negative control of genes
• Operons turned off by active repressors
• Tryptophan repressible operon
• Lactose inducible operon

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Prokaryote
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Prokaryote

• Activators
• Bind DNA
• Stimulate transcription
• Involved in glucose metabolism
• lac operon

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Prokaryote

• Activator
• Catabolite activator protein (CAP)
• Stimulates transcription of operons
• Code for enzymes to metabolize sugars
• cAMP helps CAP
• cAMP binds CAP to activate it
• CAP binds to DNA (lac Operon)

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Prokaryote

• Glucose elevated cAMP low
• cAMP not available to bind CAP
• Does not stimulate transcription
• Bacteria use glucose
• Preferred sugar over others.

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Prokaryote

• lac operon
• Regulated by positive negative control
• Low lactose
• Repressor blocks transcription
• High lactose
• Allolactose binds repressor
• Transcription happens

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Prokaryote

• lac operon
• Glucose also present
• CAP unable to bind
• Transcription will proceed slowly
• Glucose absent
• CAP binds promoter
• Transcription goes quickly

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Eukaryote gene expression

• All cells in an organism have the same genes
• Some genes turned on
• Others remain off
• Leads to development of specialized cells
• Cellular differentiation

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Eukaryote gene expression

• Gene expression assists in regulating development
  
• Homeostasis
• Changes in gene expression in one cell helps
  entire organism

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Control of gene expression

• Chromosome structure
• Transcriptional control
• Posttranscriptional control

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Fig. 18-6
Signal
NUCLEUS
Chromatin
Chromatin modification
DNA
Gene available for transcription
Gene
Transcription
Exon
RNA
Primary transcript
Intron
RNA processing
Tail
mRNA in nucleus
Cap
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Translation
Degradation of mRNA
Polypeptide
Protein processing
Active protein
Degradation of protein
Transport to cellular destination
Cellular function
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Eukaryotes

• 1. DNA is organized into chromatin
• 2. Transcription occurs in nucleus
• 3. Each gene has its own promoter

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Chromatin structure

• DNA is tightly packaged
• Heterochromatin
• Tightly packed
• Euchromatin
• Less tightly packed
• Influences gene expression
• Promoter location
• Modification of histones

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Chromatin structure

• Histone acetylation
• Acetyl groups (-COCH3)
• Attach to Lysines in histone tails
• Loosen packing
• Histone methylation
• Methyl groups (-CH3)
• Tightens packing

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Fig. 18-7
Histone tails
Amino acids available for chemical modification
DNA double helix
(a) Histone tails protrude outward from a
nucleosome
Acetylated histones
Unacetylated histones
(b) Acetylation of histone tails promotes loose
chromatin structure that permits transcription
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Chromatin structure

• Methylation of bases (cytosine)
• Represses transcription
• Embryo development

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Eukaryotes

• Epigenetic change
• Chromatin modifications
• Change in gene expression
• Passed on to the next generation
• Not a DNA sequence change

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Transcription control

• RNA polymerase must bind DNA
• Proteins regulate by binding DNA
• RNA polymerase able to bind or not
• Stimulates transcription or blocks it

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Fig. 18-8-3
Poly-A signal sequence
Enhancer (distal control elements)
Proximal control elements
Termination region
Exon
Exon
Exon
Intron
Intron
DNA
Downstream
Upstream
Promoter
Transcription
Exon
Exon
Exon
Intron
Intron
Primary RNA transcript
Cleaved 3? end of primary transcript
5?
RNA processing
Poly-A signal
Intron RNA
Coding segment
mRNA
3?
Start codon
Stop codon
Poly-A tail
3? UTR
5? Cap
5? UTR
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Eukaryotes

• Transcription
• RNA Polymerase
• Transcription factors (regulatory proteins)
• General transcription factors (initiation
  complex)
• Specific transcription factors

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Eukaryotes

• Initiation of transcription
• Activator proteins
• Activator binds the enhancers
• Enhancers (DNA sequences)
• Interacts with the transcription factors
• Binds to the promoter
• RNA polymerase binds and transcription begins

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Fig. 18-9-2
Promoter
Activators
Gene
DNA
Distal control element
Enhancer
TATA box
General transcription factors
DNA-bending protein
Group of mediator proteins
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Fig. 18-9-3
Promoter
Activators
Gene
DNA
Distal control element
Enhancer
TATA box
General transcription factors
DNA-bending protein
Group of mediator proteins
RNA polymerase II
RNA polymerase II
Transcription initiation complex
RNA synthesis
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Eukaryotes
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Fig. 18-10
Enhancer
Promoter
Albumin gene
Control elements
Crystallin gene
LENS CELL NUCLEUS
LIVER CELL NUCLEUS
Available activators
Available activators
Albumin gene not expressed
Albumin gene expressed
Crystallin gene not expressed
Crystallin gene expressed
(b) Lens cell
(a) Liver cell
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Post transcriptional control

• RNA processing
• Primary transcript
• Exact copy of the entire gene
• RNA splicing
• Introns removed from the mRNA
• snRNPs (small nuclear ribonulceoproteins)

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Post transcriptional control

• Splicing plays a role in gene expression
• Exons can be spliced together in different ways.
• Leads to different polypeptides
• Originated from same gene

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Post transcriptional control

• Example in humans
• Calcitonin CGRP
• Hormones released from different organs
• Derived from the same transcript

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Fig. 18-11
Exons
DNA
Troponin T gene
Primary RNA transcript
RNA splicing
or
mRNA
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Post transcriptional control
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Post transcriptional control

• Transport of transcript
• Passes through nuclear pores
• Active transport
• Cannot pass until all splicing is done

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Post transcriptional control

• mRNA degradation
• Life span
• Some can last hours, a few weeks
• mRNA for hemoglobin survive awhile

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Post transcriptional control

• Translation of RNA
• Translation factors are necessary
• Regulate translation
• Translation repressor proteins
• Stop translation
• Bind transcript
• Prevents it from binding to the ribosome

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Post transcriptional control

• Ferritin (iron storage)
• Aconitase
• Translation repressor protein
• Binds ferritin mRNA
• Iron will bind to aconitase
• Aconitase releases the mRNA
• Ferritin production increases

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Post transcriptional control

• Protein modification
• Phosphorylation
• Other alterations can affect the activity of
  protein
• Insulin
• Starts out as a larger molecule
• Cut into more active sections

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Post transcriptional control

• Protein modification
• Degradation
• Protein is marked by small protein
• Protein complex then breaks down proteins
• Proteasomes

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Post transcriptional control
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Fig. 18-UN4
Chromatin modification
Transcription
Genes in highly compacted chromatin are
generally not transcribed.
Regulation of transcription initiation DNA
control elements bind specific transcription
factors.
Histone acetylation seems to loosen chromatin
structure, enhancing transcription.
Bending of the DNA enables activators to contact
proteins at the promoter, initiating transcription
.
DNA methylation generally reduces transcription.
Coordinate regulation
Enhancer for liver-specific genes
Enhancer for lens-specific genes
Chromatin modification
Transcription
RNA processing
Alternative RNA splicing
RNA processing
Primary RNA transcript
Translation
mRNA degradation
or
mRNA
Protein processing and degradation
Translation
Initiation of translation can be controlled via
regulation of initiation factors.
mRNA degradation
Each mRNA has a characteristic life
span, determined in part by sequences in the 5?
and 3? UTRs.
Protein processing and degradation
Protein processing and degradation by
proteasomes are subject to regulation.
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Post transcriptional control

• Most gene regulation-transcription
• New discovery
• Small RNAs
• 21-28 nucleotides long
• Play a role in gene expression
• New transcript before leaving the nucleus

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Post transcriptional control

• RNA interference
• RNA forming double stranded loops from newly
  formed mRNA
• Loops are formed
• Halves have complementary sequences
• Loops inhibit expression of genes
• Where double RNA came from

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Post transcriptional control

• Dicer
• Cuts double stranded RNA into smaller RNAs
  called
• microRNA (miRNA)
• Small interfering RNA (siRNAs)

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Fig. 18-13
Hairpin
miRNA
Hydrogen bond
Dicer
miRNA
miRNA- protein complex
3?
5?
(a) Primary miRNA transcript
Translation blocked
mRNA degraded
(b) Generation and function of miRNAs
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Post transcriptional control

• miRNAs bind mRNA
• Prevents translation
• siRNAs breaks apart mRNA before its translated

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Post transcriptional control

• siRNAs play a role in heterochromatin formation
• Block large regions of the chromosome
• Small RNAs may also block transcription of
  specific genes

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Fig. 18-UN5
Chromatin modification
Small RNAs can promote the formation
of heterochromatin in certain regions, blocking
transcription.
Chromatin modification
Transcription
Translation
RNA processing
miRNA or siRNA can block the translation of
specific mRNAs.
Translation
mRNA degradation
Protein processing and degradation
mRNA degradation
miRNA or siRNA can target specific mRNAs for
destruction.
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Embryonic development

• Zygote gives rise to many different cell types
• Cells ?tissues ?
• organs ? organ systems
• Gene expression
• Orchestrates developmental programs of animals

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Fig. 18-14a
(a) Fertilized eggs of a frog
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Embryonic development

• Zygote to adult results
• Cell division
• Cell differentiation
• Cells become specialized in structure function
• Morphogenesis
• creation of from
• Body arrangement

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Fig. 47-6
(a) Fertilized egg
(b) Four-cell stage
(c) Early blastula
(d) Later blastula
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Fig. 47-1
1 mm
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Fig. 46-17
(c) 20 weeks
(a) 5 weeks
(b) 14 weeks
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Embryonic development

• All cells same genome
• Differential gene expression
• Genes regulated differently in each cell type

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Fig. 18-10
Enhancer
Promoter
Albumin gene
Control elements
Crystallin gene
LENS CELL NUCLEUS
LIVER CELL NUCLEUS
Available activators
Available activators
Albumin gene not expressed
Albumin gene expressed
Crystallin gene not expressed
Crystallin gene expressed
(b) Lens cell
(a) Liver cell
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Embryonic development

• Specific activators
• Materials in egg cytoplasm
• Not homogeneous
• Set up gene regulation
• Carried out as cells divide

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Embryonic development

• Cytoplasmic determinants
• Maternal substances in the egg
• Influence early development
• Zygote divides by mitosis
• Cells contain different cytoplasmic determinants
• Leads to different gene expression

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Fig. 18-15a
Unfertilized egg cell
Sperm
Nucleus
Fertilization
Two different cytoplasmic determinants
Zygote
Mitotic cell division
Two-celled embryo
(a) Cytoplasmic determinants in the egg
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Embryonic development

• Environment around cell influences development
• Induction
• Signals from nearby embryonic cells
• Cause transcriptional changes in target cells
• Interactions between cells induce differentiation
  of specialized cell types

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Fig. 18-15b
NUCLEUS
Early embryo (32 cells)
Signal transduction pathway
Signal receptor
Signal molecule (inducer)
(b) Induction by nearby cells
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Embryonic development

• Determination
• Observable differentiation of a cell
• Commits a cell to its final fate
• Cell differentiation is marked by the production
  of tissue-specific proteins
• Gives cell characteristic structure function

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Embryonic development

• Myoblasts
• Produce muscle-specific proteins
• Form skeletal muscle cells
• MyoD
• One of several master regulatory genes
• Produces proteins
• Commit cells to becoming skeletal muscle

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Embryonic development

• MyoD protein
• Transcription factor
• Binds to enhancers of various target genes
• Causes expression

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Fig. 18-16-1
Nucleus
Master regulatory gene myoD
Other muscle-specific genes
DNA
Embryonic precursor cell
OFF
OFF
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Fig. 18-16-2
Nucleus
Master regulatory gene myoD
Other muscle-specific genes
DNA
Embryonic precursor cell
OFF
OFF
OFF
mRNA
MyoD protein (transcription factor)
Myoblast (determined)
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Fig. 18-16-3
Nucleus
Master regulatory gene myoD
Other muscle-specific genes
DNA
Embryonic precursor cell
OFF
OFF
OFF
mRNA
MyoD protein (transcription factor)
Myoblast (determined)
mRNA
mRNA
mRNA
mRNA
Myosin, other muscle proteins, and cell
cycle blocking proteins
MyoD
Another transcription factor
Part of a muscle fiber (fully differentiated cell)
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Embryonic development

• Pattern formation
• Development of spatial organization of tissues
  organs
• Begins with establishment of the major axes
• Positional information
• Molecular cues control pattern formation
• Tells a cell its location relative to the body
  axes neighboring cells

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Fruit fly

• Unfertilized egg contains cytoplasmic
  determinants
• Determines the axes before fertilization
• After fertilization,
• Embryo develops into a segmented larva with three
  larval stages

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Fig. 18-17a
Thorax
Head
Abdomen
0.5 mm
Dorsal
Right
BODY AXES
Posterior
Anterior
Left
Ventral
(a) Adult
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Fig. 18-17b
Follicle cell
Egg cell developing within ovarian follicle
1
Nucleus
Egg cell
Nurse cell
Egg shell
Unfertilized egg
2
Depleted nurse cells
Fertilization Laying of egg
Fertilized egg
3
Embryonic development
Segmented embryo
4
0.1 mm
Body segments
Hatching
Larval stage
5
(b) Development from egg to larva
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Fruit fly

• Homeotic genes
• Control pattern formation in late embryo,larva
  and adult

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Fig. 18-18
Eye
Leg
Antenna
Wild type
Mutant
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Fruit fly

• Maternal effect genes
• Encode for cytoplasmic determinants
• Initially establish the axes of the body of
  Drosophila
• Egg-polarity genes
• Maternal effect genes
• Control orientation of the egg
• Consequently the fly

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Fruit Fly

• Bicoid gene
• Maternal effect gene
• Affects the front half of the body
• An embryo whose mother has a mutant bicoid gene
• Lacks the front half of its body
• Duplicate posterior structures at both ends

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Fig. 18-19a
EXPERIMENT
Tail
Head
A8
T1
T2
A7
T3
A6
A1
A5
A2
A3
A4
Wild-type larva
Tail
Tail
A8
A8
A7
A7
A6
Mutant larva (bicoid)
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