B. The trp Operon in E. coli

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B. The trp Operon in E. coli
This operon is responsible for making proteins
that PRODUCE the amino acid tryptophan. If trp
is low, then genes are on And trp is made As
trp increases, it binds to repressor,
ACTIVATING the repressor so that it can bind to
the operator turning genes OFF. This
regulation is also mediated through stem-loop
formation in the leader-attenuator region of
the m-RNA product.
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m-RNA
B. The trp Operon in E. coli
This regulation is mediated through stem-loop
formation in the leader-attenuator region of
the m-RNA product. If trp is low Ribosome
read to the double trp codons, but trp is low,
so they are slow to add into the ribosome so
translation stalls in the 1 region so 2 binds
with 3. The 2-3 loop forms does not destabilize
transcription transcription continues and the
rest of the m-RNA is made, and translation
continues, also.... GENES ON for trp SYNTHESIS
m-RNA
3
m-RNA
B. The trp Operon in E. coli
This regulation is mediated through stem-loop
formation in the leader-attenuator region of
the m-RNA product. If trp is high Ribosome
read through the trp codons, adding trp amino
acid to the protein chain and preventing the 2-3
loop. 3 binds with 4, forming the loop that
terminates transcription even before trp is
high enough to activate the repressor.
Transcription is terminated in the attenuator
region.
m-RNA
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• XII. Gene Regulation
• The lac Operon in E. coli
• B. The trp Operon in E. coli
• C. Regulation in Eukaryotes
• Regulation in eukaryotes is more complex, as it
  regulates the specialization of different
  tissues, the developmental changes of organisms
  over time, and genetic responses to the
  environment.
• As such, it is not surprising that the patterns
  of regulation are much more complex often as a
  consequence of greater structural complexity of
  chromosomes and genes.

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C. Regulation in Eukaryotes - Histones affect
accessibility of a gene
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C. Regulation in Eukaryotes - Histones affect
accessibility of a gene - Methylation causes
condensation of genes and chromosomes
Imprinting Heterochromatin (highly repetitive
DNA) Barr Bodies (X inactivation)
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C. Regulation in Eukaryotes - Histones affect
accessibility of a gene - Methylation causes
condensation of genes and chromosomes -
Transcription is regulated by transcription
factors that increase (enhancers) or decrease
(silencers) the ability of the RNA polymerase to
bind to the promoter and begin transcription.
Because genes are regulated by multiple
transcription factors, it means one gene can be
turned on by many different signals and become
associated with many enzymatic pathways in a
cell/organism. And, binding can be modulated
not just on/off but on by degrees
8
C. Regulation in Eukaryotes - Histones affect
accessibility of a gene - Methylation causes
condensation of genes and chromosomes -
Transcription is regulated by transcription
factors that increase (enhancers) or decrease
(silencers) the ability of the RNA polymerase to
bind to the promoter and begin transcription.
They tend to have particular structures that bind
DNA in specific ways helix-turn-helix, zinc
fingers, leucine zippers
9

• C. Regulation in Eukaryotes
• Transcription can also be regulated by small
  pieces of RNA called si-RNA (small interfering
  RNA) and mi-RNA (microRNA). These molecules are
  short RNA sequences that bond with m-RNA and
  either cleave it (si-RNA) or just bind to it and
  block translation (mi-RNA). They can also
  initiate methylation of promoters and turn genes
  off.
• This process is called RNA interference or RNAi

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•  
•  
• High resolution image (pdf 2,5 Mb) 
•  

C. Regulation in Eukaryotes Fire and Mello -1998
(Nobel in Phys or Medicine 2006)
RISC RNA-induced Silencing Complex Binds to
m-RNA and splices it.
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•  
•  
• High resolution image (pdf 2,5 Mb) 
•  

• C. Regulation in Eukaryotes
• There are two ways that double-stranded RNAs
  naturally occur through viral infection or
  transcription of mi-RNA genes.
• Unclear whether this evolved first as a mechanism
  to regulate gene production, or as an adaptation
  to resist viral infection.

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• C. Regulation in Eukaryotes
• RITS target promoters of specific genes or larger
  regions of chromatin. Remodeling of chromatin
  turns genes off, often by inducing methylation.
• Important in imprinting
• Both pathways can inhibit production of
  transcription factors, too, and affect other
  regulatory pathways.

RITS RNA induced initation of transcription
silencing complex
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C. Regulation in Eukaryotes - Alternate Splicing
Pathways, regulated by intronic ribozymes and
spliceosomes, can make different protein
products
A calcium regulator in the thyroid
A hormone made in the brain
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C. Regulation in Eukaryotes - The initial
polypeptide product can be spliced differently,
too, to produce different functional proteins
from the same initial polypeptide. And the
methionine is cleaved and it is coplexed with
other molecules (quaternary protein, lipoprotein,
glycoprotein, riboprotein).
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Chromatin remodeling
Polymerase binding
transcription
M-RNA processing
translation
Post-translational modifications
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zygote
mitosis
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Heredity, Gene Regulation, and Development
Mutation A. Overview
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Mutation A. Overview 1) A mutation is a change
in the genome of a cell.
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Mutation A. Overview 1) A mutation is a change
in the genome of a cell. 2) Some
mutations occur during DNA repair, or after DNA
is damaged by a mutagen. These changes may
affect how that particular cell works. When/if
that cell divides, then this defect will be
propagated to the daughter cells in that body
tissue. These are somatic mutations.
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Mutation A. Overview 1) A mutation is a change
in the genome of a cell. 2) Some
mutations occur during DNA repair, or after DNA
is damaged by a mutagen. These changes may
affect how that particular cell works. When/if
that cell divides, then this defect will be
propagated to the daughter cells in that body
tissue. These are somatic mutations. 3)
Some errors occur in DNA replication that
precedes cell division these changes are passed
to the daughter cells in that body tissue. These
are somatic mutations, too.
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Mutation A. Overview 1) A mutation is a change
in the genome of a cell. 2) Some
mutations occur during DNA repair, or after DNA
is damaged by a mutagen. These changes may
affect how that particular cell works. When/if
that cell divides, then this defect will be
propagated to the daughter cells in that body
tissue. These are somatic mutations. 3)
Some errors occur in DNA replication that
precedes cell division these changes are passed
to the daughter cells in that body tissue. These
are somatic mutations, too. 4) Some
mutations occur during meiosis, and produce
mutant gametes. These are the heritable
mutations that we will focus on.
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• VI. Mutation
• Overview
• A change in the genome
• Occurs at four scales of genetic organization
• 1 Change in the number of sets of chromosomes (
  change in ploidy)
• 2 Change in the number of chromosomes in a set
  (aneuploidy)
• 3 Change in the number and arrangement of genes
  on a chromosome
• 4 Change in the nitrogenous base sequence
  within a gene

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• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes

Triploidy occurs in 2-3 of all human
pregnancies, but almost always results in
spontaneous abortion of the embryo. Some
triploid babies are born alive, but die shortly
after. Syndactyly (fused fingers), cardiac,
digestive tract, and genital abnormalities occur.
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• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes
• Mechanism 1 Complete failure of Meiosis
• - if meiosis fails, reduction does not occur and
  a diploid gamete is produced. This can occur
  because of failure of homologs OR sister
  chromatids to separate in Meiosis I or II,
  respectively.

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• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes
• Mechanism 1 Complete failure of Meiosis
• - if meiosis fails, reduction does not occur and
  a diploid gamete is produced. This can occur
  because of failure of homologs OR sister
  chromatids to separate in Meiosis I or II,
  respectively.

26

• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes
• Mechanism 1 Complete failure of Meiosis
• - if meiosis fails, reduction does not occur and
  a diploid gamete is produced. This can occur
  because of failure of homologs OR sister
  chromatids to separate in Meiosis I or II,
  respectively.
• - this results in a single diploid gamete, which
  will probably fertilize a normal haploid gamete,
  resulting in a triploid offspring.
• negative consequences of Triploidy
• 1) quantitative changes in protein production
  and regulation.
• 2) cant reproduce sexually cant produce
  gametes if you are 3n.

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• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes
• Mechanism 1 Complete failure of Meiosis
• negative consequences of Triploidy
• 1) quantitative changes in protein production
  and regulation.
• 2) cant reproduce sexually cant produce
  gametes if you are 3n.
• 3) but, some organisms can survive, and
  reproduce parthenogenetically (mitosis)

Like this Blue-spotted Salamander A. laterale,
which has a triploid sister species, A.
tremblayi
A. tremblayi is a species that consists of 3n
females that reproduce clonally laying 3n eggs
that divide without fertilization.
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• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes
• Mechanism 1 Complete failure of Meiosis
• Mechanism 2 Failure of Mitosis in
  Gamete-producing Tissue

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2n
1) Consider a bud cell in the flower bud of a
plant.
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2n
4n
1) Consider a bud cell in the flower bud of a
plant.
2) It replicates its DNA but fails to divide...
Now it is a tetraploid bud cell.
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2n
4n
1) Consider a bud cell in the flower bud of a
plant.
2) It replicates its DNA but fails to divide...
Now it is a tetraploid bud cell.
3) A tetraploid flower develops from this
tetraploid cell eventually producing 2n SPERM
and 2n EGG
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How do we define species? A group of
organisms that reproduce with one another and are
reproductively isolated from other such
groups (E. Mayr biological species concept)
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How do we define species? Here, the
tetraploid population is even reproductively
isolated from its own parent speciesSo
speciation can be an instantaneous genetic
event
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• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes
• Mechanism 1 Complete failure of Meiosis
• Mechanism 2 Complete failure of Mitosis
• Mechanism 3 Allopolyploidy - hybridization

Polyploidy occurs here creating a cell with
homologous sets
Black Mustard
gametes
2n 16
n 8
2n 34
n 17
2n 18
n 9
Fertilization produces a cell with non-homologous
chromosomes
New Species
Cabbage
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X
Spartina alterniflora from NA colonized Europe
Spartina maritima native to Europe
Sterile hybrid Spartina x townsendii
Allopolyploidy 1890s
Spartina anglica an allopolyploid and a
worldwide invasive outcompeting native species
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• VI. Mutation
• Overview
• Changes in Ploidy
• - These are the most dramatic changes, adding a
  whole SET of chromosomes
• Mechanism 1 Complete failure of Meiosis
• Mechanism 2 Complete failure of Mitosis
• Mechanism 3 Allopolyploidy - hybridization
• The Frequency of Polyploidy
• For reasons we just saw, we might expect
  polyploidy to occur more frequently in
  hermaphroditic species, because the chances of
  jumping the triploidy barrier to reproductive
  tetraploidy are more likely. Over 50 of all
  flowering plants are polyploid species many
  having arisen by this duplication of chromosome
  number within a lineage.