Nerve activates contraction

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CHAPTER 19THE ORGANIZATION AND CONTROL OF
EUKARYOTIC GENOMES

• gt Larger than prokaryotes
• Not all 25,000 genes are active in all cells

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Junk DNA anyone?

• Prokaryotes- most of the DNA in a genome codes
  for protein (or tRNA and rRNA), with a small
  amount of noncoding DNA, primarily regulators.
• Eukaryotes - most of the DNA (about 97 in
  humans) does not code for protein or RNA.

• Only 25,000 genes in humans - 3 of total DNA in
  cell (YIKES!)
• Rest of it (97) - junk????? (noncoding DNA)

96 similar to humans)
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Noncoding DNA and what it does in the
eukaryotic genome

• 1) Some noncoding regions are regulatory
  sequences (these are promotors and enhancers that
  can increase binding of RNA polymerase to DNA).
• 2) Other are introns.
• 3) Finally, even more of it consists of
  repetitive DNA, present in many copies in the
  genome.

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REPPPPETITIVE DNA IN EUKARYOTES

• Know 2 types of Repetitive DNA
• 1)TANDEMLY REPETITIVE DNA (AKA SATELLITE DNA - 3
  types) - 10 to 15 of DNA
• 2) INTERSPERSED REPETITIVE DNA - 25 - 40 of DNA

GTTACGTTACGTTAC.repeated 10 to 10 million times
(Satellite DNA)
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REPPPPETITIVE DNA IN EUKARYOTES

• 1) SATELLITE DNA/TANDEMLY REPETITIVE DNA
• These sequences (1 to 10 base pairs) are repeated
  up to a million times in series.
• GTTACGTTACGTTAC.
• 3 types
• a) Regular Satellite -100,000 - 10 mill
• b) Minisatellite -100 -100,000 repeats
• c) Microsatellite - 10 to 100 repeats -
• Very important for forensics - helps figure out
  uniqueness of a persons DNA

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• A number of genetic disorders are caused by
  abnormally long stretches of tandemly repeated
  nucleotide triplets within the affected gene.

• CAG
• Repeat

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You know that antisocial neighbor - May be a
microsatellite problem!
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• Satellite DNA plays a structural role at
  telomeres and centromeres. This is important!
  You dont want non-repetitive DNA in telomeres
  because?

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CSI Lab on this coming up- Microsatellites
more repeats but really short!

• Are only 1-10 nucleotides long and are repeated
  only 10-100 times in the genome
• Used in DNA fingerprinting (forensics)

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• What, more junk?
• (2) About 25-40 of most mammalian genomes
  consists of interspersed repetitive DNA.
• -One common family of interspersed repetitive
  sequences, Alu elements, is transcribed into RNA
  molecules with unknown roles in the cell.
• -Alu sequences may help alternate RNA splicing
• -Transposons are interspersed repetitive DNA

Table 19.1 bottom
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Out of 25,000 genes what gets expressed depends
upon

• Type of cell Not all genes are expressed in all
  cells (epigenetics controls it)
• Development period During embryonic development
  certain genes may be expressed that are not
  expressed in adults (and viceversa)

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Gene families - collection of genes that may be
identical/nonidentical
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Gene families have evolved by duplication of
ancestral genes

• Most genes are present as a single copy per
  haploid set of chromosomes
• Multigene families exist as a collection of
  identical or very similar genes (exceptions).
• These likely evolved from a single ancestral
  gene.
• The members of multigene families may be
  clustered or dispersed in the genome.

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• Identical genes are multigene families that are
  clustered tandemly.

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• Evolution - first duplicate a gene and then
  mutate the copy result original copy is still
  there, mutated gene - could make a new protein
  new function (natural selection acts on it)
• Nonidentical genes have diverged since their
  initial duplication event.

Pseudogenes- DNA segments that have sequences
similar to real genes but that do not yield
functional proteins - remnants of evolution or?
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Did you know your genome changes continually in
your lifetime?

• 1) Rare mutations (between 1/106 and 1/105
  nucleotides )
• 2) Gene amplification selective DNA replication
  of some genes to increase protein expression (ex.
  after chemotherapy)
• 3) Transposons/
• Retrotransposons-
• (Jumping genes)
• 50 - Corn
• 10 Human
• (Not inherited)
• 4)Gene rearrangement

Transposon moved into the purple color gene
destroying its activity
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• Altering genomes during your lifetime? continued
• Rare mutations
• Gene amplification - temporary increase
  (selective loss also possible) in number of gene
  copies
• Transposons and retrotransposons
• Gene rearrangement in Immunoglobin genes

Fig. 19.5
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B lymphocytes (WBC) produce immunoglobins, or
antibodies, that specifically recognize and
combat viruses, bacteria, and other invaders.

• Millions of types of Antibodies can be produced
  depending on what the infectious agent is - how?
• Immunoglobins have constant and variable region
• 100s of gene segments code for the variable
  region of the antibody.
• DNA segments are put together to create an
  endless combination of constant and variable
  regions - gene rearrangement occurs in your
  lifetime!

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TRANSLATION
TRANSCRIPTION
Promotor
RNA Polymerase makes premRNA using the elves -
transcription factors (proteins)
Many protein factors are involved in
translation as well
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How is gene expression controlled?

• That is if/what protein is made? How can you
  control this?

• Levels of control goals..
• 1) Changing DNA physically gt mRNA making
  affected
• 2) Changing access to DNA Promotor
• 3) If mRNA is made How long mRNA hangs around
  change which protein is made from one mRNA -
  (splicing) dont use the mRNA
• 4) Change/destroy the protein after its made

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How is gene expression controlled in you?
(IMPORTANT)

• When is the gene active (on or off)? That is what
  protein is made? How can you control this?

• Gene expression control which genes are on
• Levels of control
• 1) chromatin (DNA) packing and chromatin
  modification - change access sites on DNA for RNA
  Polymerase so that its binding decreases/increases
  (epigenetics - layer of control above the genome
  - NOVA Video)
• 2) Transcription - when DNA makes mRNA
• 3) Post-transcriptional - RNA processing,
  translation
• 4) Post-translational - various alterations to
  the protein product.

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Fig. 19.7
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• 1a) Level of packing is one way that gene
  expression is regulated.
• Densely packed areas are inactivated.
  (Heterochromatin)
• Loosely packed areas are being actively
  transcribed. (Euchromatin) -

- during mitosis
- during Interphase
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Chromatin structure is based on successive levels
of DNA packing

INTERPHASE

• Interphase - chromatin fibers highly extended
• Mitosis - chromatin coils and condenses to form
  short, thick chromosomes.

MITOSIS

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• Histone proteins are responsible for the first
  level of DNA packaging.
• Their positively charged amino acids bind tightly
  to negatively charged DNA.

Which stage do you see beads on a string?
(Interphase) Are genes active? - Yes transcribed
into mRNA!
Beads on a string a nucleosome, in which DNA
winds around a core of histone proteins
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• Next level of packing - 30 nm solenoid fiber
  nucleosome fiber
• Has (DNA HISTONES) with 6 nucleosomes per turn

Which stage do you see 30 nm fiber?
(Mitosis) Are genes active? - Yes transcribed
into mRNA!
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• The 30 nm fiber forms looped domains attached to
  a scaffold of nonhistone proteins.

Which stage do you see looped domains?
(Mitosis) Are genes active? -No
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1b) Chromatin modifications (epigenetics)

• Chemical modifications of DNA bases
• A) DNA methylation is the attachment by specific
  enzymes of methyl groups (-CH3) Inactive DNA is
  highly methylated compared to DNA that is
  actively transcribed.
• Genomic imprinting is related to DNA methylation

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DNA Methylation - add a methyl group to make DNA
less accessibleto RNA Polymerase
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1b) Chromatin modifications

• B) Histone acetylation (addition of an acetyl
  group -COCH3) and deacetylation
• Acetylated histones grip DNA less tightly ?
• More access to RNA Polymerase! SO,.

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Epigenetics - DNA methylation and histone
acetylation may be responsible for a lot of
traits that are not just related to whether you
have the gene/not. Example If your gene is
methylated you may never express the trait!
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2) Control of Transcription very important - to
make or not make mRNA
Control elements - noncoding DNA segments that
regulate transcription by binding transcription
factors that are needed for RNA Polymerase
binding. (TATA Box -Promotor, Activators in
bacteria - Enhancers in Eukaryotes, Repressors
in bacteria - Silencers in Eukaryotes)
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• How can a DNA control element 100s of basepairs
  upstream of a gene regulate the access to RNA
  Polymerase?
• Bending of DNA enables transcription factors,
  activators (like steroid hormones), bound to
  enhancers to contact the complex at the promoter.

Mostly positive gene regulation in eukaryotes!
Fig. 19.9
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• The hundreds of eukaryotic transcription factors
  follow only a few basic structural principles.
• Each protein generally has a DNA-binding domain
  that binds to DNA and a protein-binding domain
  that recognizes other transcription factors.

Fig. 19.10
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3) Post-transcriptional mechanisms - so mRNA is
made, what next?

• A) RNA processing alternative splicing -
  controls which protein is made from one mRNA -
  mix-n-match introns/exons

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3) Post-transcriptional mechanisms

• B) Life span of a mRNA molecule
• Prokaryotic mRNA molecules degraded by enzymes
  after only a few minutes.
• Eukaryotic mRNAs endure typically for hours or
  even days or weeks.

G
AAAAA
L
T
5 Cap Leader Trailer Poly A tail
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3) Post-transcriptional mechanisms

• C) Translation - can be blocked by regulatory
  proteins that bind to 5 leader region of mRNA.
• (prevents attachment of mRNA to ribosomes)
• Protein factors required to initiate translation
  simultaneous control of translation of all the
  mRNA in a cell.

G
AAAAA
L
T
5 Cap Leader Trailer Poly A tail
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4) Post-translational mechanisms

• Processing of polypeptides to yield functional
  proteins.
• This may include cleavage, chemical
  modifications, and transport to the appropriate
  destination.
• Regulation may occur at any of these steps.

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• The cell limits the lifetimes of normal proteins
  by selective degradation.
• Proteins intended for degradation are marked by
  the attachment of ubiquitin proteins.
• Giant proteosomes recognize the ubiquitin and
  degrade the tagged protein.

Fig. 19.12
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CANCER REVIEW- read on your own - use these
animations
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Cancer results from genetic changes that affect
the cell cycle

• Cell cycle CONTROL events dont work
• Spontaneous mutations or environmental influences
  (carcinogens)
• Cancer-causing genes oncogenes (retroviruses),
  proto-oncogenes (in other organisms).
• What happens when proto-oncogenes/oncogenes are
  turned ON? (Ras gene)
• Cell will divide without stopping

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• Malignant cells often have significant changes in
  chromosomes

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Fig. 19.13
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Are there genes that prevent cancer?

• Tumor-suppressor genes -normal products inhibit
  cell division, repair DNA, control adhesion
  (p53).
• Mutations to these tumor suppressor genes
  cancer

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Oncogene proteins and faulty tumor-suppressor
proteins
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• The p53 gene, named for its 53,000-dalton protein
  product, is often called the guardian angel of
  the genome.
• Damage to the cells DNA acts as a signal that
  leads to expression of the p53 gene.
• The p53 protein is a transcription factor for
  several genes.
• It can activate the p21 gene, which halts the
  cell cycle.
• It can turn on genes involved in DNA repair.
• When DNA damage is irreparable, the p53 protein
  can activate suicide genes whose protein
  products cause cell death by apoptosis.

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3. Multiple mutations underlie the development of
cancer

• More than one somatic mutation is generally
  needed to produce the changes characteristic of a
  full-fledged cancer cell.
• If cancer results from an accumulation of
  mutations, and if mutations occur throughout
  life, then the longer we live, the more likely we
  are to develop cancer.

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• Colorectal cancer, with 135,000 new cases in the
  U.S. each year, illustrates a multi-step cancer
  path.
• The first sign is often a polyp, a small benign
  growth in the colon lining with fast dividing
  cells.
• Through gradual accumulation of mutations that
  activate oncogenes and knock out tumor-suppressor
  genes, the polyp can develop into a malignant
  tumor.

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Fig. 19.15
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• About a half dozen DNA changes must occur for a
  cell to become fully cancerous.
• These usually include the appearance of at least
  one active oncogene and the mutation or loss of
  several tumor-suppressor genes.
• Since mutant tumor-suppressor alleles are usually
  recessive, mutations must knock out both alleles.
  
• Most oncogenes behave as dominant alleles.
• In many malignant tumors, the gene for telomerase
  is activated, removing a natural limit on the
  number of times the cell can divide.

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• Viruses, especially retroviruses, play a role is
  about 15 of human cancer cases worldwide.
• These include some types of leukemia, liver
  cancer, and cancer of the cervix.
• Viruses promote cancer development by integrating
  their DNA into that of infected cells.
• By this process, a retrovirus may donate an
  oncogene to the cell.
• Alternatively, insertion of viral DNA may disrupt
  a tumor-suppressor gene or convert a
  proto-oncogene to an oncogene.

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• The fact that multiple genetic changes are
  required to produce a cancer cell helps explain
  the predispositions to cancer that run in some
  families.
• An individual inheriting an oncogene or a mutant
  allele of a tumor-suppressor gene will be one
  step closer to accumulating the necessary
  mutations for cancer to develop.

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• Geneticists are devoting much effort to finding
  inherited cancer alleles so that predisposition
  to certain cancers can be detected early in life.
• About 15 of colorectal cancers involve inherited
  mutations, especially to DNA repair genes or to
  the tumor-suppressor gene APC.
• Normal functions of the APC gene include
  regulation of cell migration and adhesion.
• Between 5-10 of breast cancer cases, the 2nd
  most common U.S. cancer, show an inherited
  predisposition.
• Mutations to one of two tumor-suppressor genes,
  BRCA1 and BRCA2, increases the risk of breast and
  ovarian cancer.