Gene Expression

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Gene Expression
How long you will live
Fears
Weight

• What determines the mix of proteins in a cell at
  any given time?

How you will respond to stress
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Can some acquired traits be passed on? If so how?
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How could acquired traits be passed on and can
they be changed during your life?

• Basically, you not only pass on your genes to the
  next generation, you pass on some of the signals
  attached to the DNA that control the reading of
  the genes, which can change the expression of a
  trait
• Some of these signals can be changed throughout
  life
• Some of these signals are reset in the sperm and
  egg

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Epigenetics Switching genes on and off
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Why do cells need to control gene expression?

• Different stages of development
• Differentiation
• Meet demands of the organ
• Respond to changing environment
• Respond to outside signals
• Make sure you are not wasting energy making
  things you dont need

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Eukaryotic Gene Expression

• 6 x 109 base pairs 35,000 genes
• 5-20 of genes expressed/cell
• 1000-7000 genes transcribed/cell
• Promoter marks the beginning of each gene, but
  how does cell know what genes to transcribe?
• What else controls how much protein and which
  proteins are created in a cell and what the final
  protein looks like?

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You are what you eat?!
Or even what your mother ate
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Why Genes Arent DestinyExcepts

• conditions in the womb could affect your health
  not only when you were a fetus but well into
  adulthood.
• if a pregnant woman ate poorly, her child would
  be at a significantly higher than average risk
  for cardiovascular disease as an adult.
• kids who went from normal eating to gluttony in
  a single season produced sons and grandsons who
  lived shorter lives. A single winter of
  overeating as a youngster could initiate a
  biological chain of events that would lead ones
  grandchildren to die decades earlier than their
  peers did.

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Excepts Continued

• exposed mice with genetic memory problems to an
  environment rich with toys, exercise, and extra
  attention. These mice showed significant
  improvement in long term potentiation (key to
  memory formation). Surprisingly, their offspring
  also showed LTP improvement, even when the
  offspring got no extra attention.
• sons of men who smoke in prepuberty will be at
  higher risk for obesity and other health
  problems
• In 2008, the NIH would pour 190 million into
  how and when epigentic processes control genes.

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Gene Expression Can be Controlled at Any Level of
Protein Production or Activation
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Control of Eukaryotic Gene Expression

• Availability of genes to RNA Polymerase and
  transcription factors
• 1. If DNA is too compact no gene expression
• Euchromatin normal chromatin gene expression
• Heterochromatin more condensed no expression
• Chromosomes extremely condensed no expression

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Difference in Euchromatin and Heterochromatin
Dark staining areas are heterochromatin, light
are euchromatin more euchromatin more active
the cell is always heterochromatin around the
inside of the nuclear membrane
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Inactive lymphocyte on leftActivated lymphocyte
on the right
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Availability of DNA to RNA Polymerase Continued

• 2. How close DNA is to the nucleosome and if it
  is attached to the nuclear matrix determines
  access of enzymes
• 3. Acetylation of histone proteins unwinds the
  DNA so enzymes have access
• 4. Methylation inhibits DNA expression,
  responsible for DNA imprinting (methylation
  patterns are often messed up in cancer cells)

http//learn.genetics.utah.edu/content/epigenetics
/rats/
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Availability of DNA to RNA Polymerase Continued
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II. Transcriptional Control

• 1. Controlled by regulatory proteins and
  transcription factors (Make up transcription
  initiation complex)

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Eukaryotic Genes Regulatory Elements
Movie of Transcription Initation Complex
Activators or Repressors Bind to distal control
elements
/silencer
Transcription Factors Binds to proximal control
elements AND to the promoter.
DNA Proximal Control Elements Distal
Control Elements Enhancers and
Silencers Proteins Transcription Factors
(general and specific) Activators Repressors
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Genes of same enzymatic pathway are spread out
all over the genome so how are they all
expressed at the same time?
Each gene has its own promoter but many may have
same proximal and distal control elements so 1
type of transcription factor and activator may
control many genes (in the same enzymatic
pathways)
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Another Way Transcription Is Controlled

• Steroid Hormones
• Steroids bind to a receptor and translocate into
  nucleus.
• Steroid/receptor complex binds to DNA in upstream
  regulatory elements to switch on genes.

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• III. Control of RNA Processing
• Alternative Splicing Dont know what controls
  the splicing spliceosomes bind to ends of
  introns but what identifies what are the
  introns???
• Some genes have many alternate forms due to
  splicing

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IV. Control of RNA Degredation

• Untranslated trailer of mRNA controls if
  translation lasts hrs. or weeks (may be a
  binding site for ncRNAs)
• ncRNA (non-coding RNAs)
• a. Micro RNAs
• Transcribed, folds, piece is cut off by a Dicer
  which also destroys the 2nd strand. Single
  strand combines with protein and then binds to
  and inactivates mRNAs with complementary
  sequences or causes their destruction
• b. Small Interfering RNA (same as miRNA but
  from longer pieces of RNA)
• Both mi and si RNA can recruit enzymes to form
  heterochromatin and therefore turn off
  genes

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How miRNA works
RNAi Video
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• Control of Translation
• Regulatory proteins can prevent mRNA from binding
  to the ribosome must be removed before
  translation occurs
• Initiation Factor (helps mRNA bind to ribosome)
• Example fertilization turns on initiation
  factor so get quick translation prevents
  translation until activate the initiation factor

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VI. Post-Translational Modifications

• Can prevent correct modifications or transport
• Can be modified differently by different enzymes
  in the rough ER of different kinds of cells
  (maybe different enzymes in different RER of
  different cell types?)
• VII. Protein Degredation (Proteosome chops up
  unneeded proteins tagged with ubiquitin) Dont
  know what controls speed of degredation

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VIII. Gene sequences themselves may affect
expression

• 1. Multi-Gene Families - may have multiple copies
  of the same gene (can be expressed at once or at
  different times in response to the environment)
• Examples
• genes to make rRNA (100-1000 repeats of these
  genes together)
• Genes to make hemoglobin proteins multiple
  copies are slightly different produced at
  different times during development.

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2. Transposons Jumping Genes May copy and
move or just move. May jump into a gene and
disrupt it may jump into a regulatory area and
increase or decrease production of that
protein Insertion codes for an enzyme that
cuts it out Complex has other genes
that move too Retrotransposons code for
RNA which is then copied into DNA and inserted
somewhere else in genome
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(No Transcript)
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Gene Sequences Controlling Expression Continued

• 3. Satellite DNA (short sequences repeated many
  times short tandem repeats) Makes up 10-15 of
  genome (telomeres are satellite DNA)
• Can act as transposons
• Can be extended causing genes to malfunction
• 4. Interspersed Repetitive DNA (25-40 of
  genome) 100-1000 b.p spread throughout most
  are transposons

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Neurofibromatosis
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Cause of Neurofibromatosis
Neurofibromatosis 1 (1/3000) births Mutation in
the neurofibromin gene on chromosome
17 Neurofibromin is a tumor supressor gene which
inhibits the p21 ras oncoprotein It causes neural
tumors all over the body due to uncontrolled cell
division Have also found cases where the disease
is caused by an Alu sequence jumping gene
jumps into the gene and messes it up
Alu sequence inserted in an intron of the NF1
gene The presence of the Alu sequence caused a
splicing error, which in turn caused one of the
exons to be left out of the transcribed mRNA,
thereby leading to a shift in the reading frame
and production of an abnormal protein.
Researchers have reported a growing number of
Alu-disease associations in disorders ranging
from hemophilia to breast cancer. According to
one estimate, about 0.4 of all human genetic
disorders are caused by or associated with Alu
11 of genome is Alu sequences
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5. Gene RearrangementsExample antibodies
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• 6. Gene Amplification making more copies of a
  gene when needed
• Example rRNA genes in developing embryo of
  amphibians extra copies are small circular
  pieces that are destroyed after embryonic
  development
• Example Cancer cells in response to drugs
  (amplify drug resistance genes)
• 7. Selective Gene Loss in developing embryo
  only in some cells in insects

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Gene Expression and Embryonic Development

• Cytoplasmic Determinants RNA and proteins
  unevenly distributed in the egg that signal
  development
• Induction signals from surrounding cells that
  control development
• Master regulatory genes
• turn on tissue specific genes
• to make tissue specific proteins
  

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Body Plan Patterning

• Both cytoplasmic determinants and inductive
  signals help set up positional information
• Homeotic Genes
• contain program for development of the body plan
• Are highly conserved and have same sequences
  within the genes called homeoboxes.
• Code for transcription factors and are master
  control genes

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Homeobox Genes
Homeobox 180 nucleotide segment of homeotic
genes. Conserved in all animals part of gene
that codes for part of protein that binds to the
DNA. Hox genes found in clusters on the
chromosomes. Genes are lined up in order of what
part of the body they control the formation of.
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Mutated Hox Genes
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Oncogenes

• Oncogenes cancer causing genes induced by
  viruses
• Protooncogenes normal genes that become cancer
  causing when they are
• Mutated
• Amplified
• Or move into an area with an active promoter
• Examples growth factors, cell cycle proteins,
  tumor supressors (inactivated and usually supress
  growth), cell attachment proteins

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Proto-oncogene Example

• Ras gene codes for a G-Protein (activated by a
  receptor when messenger binds and sets off a
  series of chemical reactions leading to increase
  in cell division thru the activation of
  transcription factors)
• Mutated Ras gene G protein is always on even
  when nothing is bound to receptor
• Found in 20-25 of all human tumors

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Tumor Supressor Genes

• Repair damaged DNA
• Control cell adhesion
• Inhibit the cell cycle
• Activate cell suicide if damage is unfixable
• Example p53 gene (p53 mutation found in over
  50 of human tumors)
• In response to damage it
• Halts the cell cycle
• Turns on DNA repair enzymes
• Activated apoptosis if damage cannot be repaired

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Cancer Cells vs. Normal
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BACTERIAL GENE EXPRESSION

• Allows bacteria to live in a changing
  environment.
• Operons a whole gene unit all genes necessary
  for an enzymatic pathway are lined up behind a
  promoter and operator.
• Promoter Operator Genes Term. Seq.

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Bacterial Operons

• Operator controls access to promoter for RNA
  polymerase
• Operator is always on unless a protein is bound
  to it
• Repressor binds to operator and blocks RNA
  polymerase from binding specific to the operon.

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Repressors for Operators

• For Anabolic Operons
• Repressible Operon
• Product shuts off operon by activating the
  repressor
• For Catabolic Operons
• Inducible Operon
• Substrate turns on operon by deactivating the
  repressor

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Repressor Concept
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Tryptophan Operon An example of an operon that
codes for enzymes in an anabolic pathway
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The lac operon an example of an operon coding
for enzymes in a catabolic pathway
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3-D View of the Lac Repressor
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Additional ways to activate bacterial genes

• Proteins bind to the promoter making it easier
  for RNA Polymerase to bind
• Example only want to make enyzmes to break down
  lactose if lactose is present and if there is low
  glucose available
• Low glucose high AMP
• AMP CAP (catabolic activator) together bind to
  the promoter helping polymerase to attach
• CAP regulates several metabolic pathways