Chapter 11 How Genes Are Controlled

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Chapter 11 How Genes Are Controlled
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Biology and Society Tobaccos Smoking Gun

• During the 1900s, doctors noticed that
• Smoking increased
• Lung cancer increased
• In 1996, researchers studying lung cancer found
  that, in human lung cells growing in the lab, a
  component of tobacco smoke, BPDE, binds to DNA
  within a gene called p53, which codes for a
  protein that normally helps suppress the
  formation of tumors.
• This work directly linked a chemical in tobacco
  smoke with the formation of human lung tumors.

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HOW AND WHY GENES ARE REGULATED

• Every somatic cell in an organism contains
  identical genetic instructions.
• They all share the same genome.
• So what makes them different?
• In cellular differentiation, cells become
  specialized in
• Structure
• Function
• Certain genes are turned on and off in the
  process of gene regulation.

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Patterns of Gene Expression in Differentiated
Cells

• In gene expression
• A gene is turned on and transcribed into RNA
• Information flows from
• Genes to proteins
• Genotype to phenotype
• Information flows from DNA to RNA to proteins.
• The great differences among cells in an organism
  must result from the selective expression of
  genes.

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Colorized TEM
Colorized TEM
Colorized SEM
White blood cell
Pancreas cell
Nerve cell
Gene for a glycolysis enzyme
Key
Antibody gene
Active gene
Insulin gene
Hemoglobin gene
Figure 11.1
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Gene Regulation in Bacteria

• Natural selection has favored bacteria that
  express
• Only certain genes
• Only at specific times when the products are
  needed by the cell
• So how do bacteria selectively turn their genes
  on and off?
• An operon includes
• A cluster of genes with related functions
• The control sequences that turn the genes on or
  off
• The bacterium E. coli used the lac operon to
  coordinate the expression of genes that produce
  enzymes used to break down lactose in the
  bacteriums environment.

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Lac Operon

• The lac operon uses
• A promoter, a control sequence where the
  transcription enzyme initiates transcription
• An operator, a DNA segment that acts as a switch
  that is turned on or off
• A repressor, which binds to the operator and
  physically blocks the attachment of RNA
  polymerase

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A typical operon
Regulatory gene
Promoter
Operator
Gene 1
Gene 2
Gene 3
DNA
Switches operon on or off
RNA polymerase binding site
Produces repressor that in active form attaches
to operator
Figure 11.UN05
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Operon
Genes for lactose enzymes
Regulatory gene
Promoter Operator
DNA
mRNA
RNA polymerase cannot attach to promoter
Active repressor
Protein
Operon turned off (lactose absent)
Transcription
DNA
RNA polymerase bound to promoter
mRNA
Translation
Protein
Inactive repressor
Lactose
Lactose enzymes
Operon turned on (lactose inactivates repressor)
Figure 11.2
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Gene Regulation in Eukaryotic Cells

• Eukaryotic cells have more complex gene
  regulating mechanisms with many points where the
  process can be regulated, as illustrated by this
  analogy to a water supply system with many
  control valves along the way.

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Chromosome
Unpacking of DNA
DNA
Gene
Transcription of gene
Intron
Exon
RNA transcript
Processing of RNA
Flow of mRNA through nuclear envelope
Nucleus
Cap
Tail
mRNA in nucleus
Cytoplasm
mRNA in cytoplasm
Breakdown of mRNA
Translation of mRNA
Polypeptide
Various changes to polypeptide
Active protein
Breakdown of protein
Figure 11.3-7
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The Regulation of DNA Packing

• Cells may use DNA packing for long-term
  inactivation of genes.
• X chromosome inactivation
• Occurs in female mammals
• Is when one of the two X chromosomes in each cell
  is inactivated at random
• All of the descendants will have the same X
  chromosome turned off.
• If a female cat is heterozygous for a gene on the
  X chromosome
• About half her cells will express one allele
• The others will express the alternate allele

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Two cell populations in adult cat
Early embryo
Active X
Orange fur
Inactive X
Cell division and X chromosome inactivation
X chromosomes
Allele for black fur
Allele for orange fur
Inactive X
Black fur
Active X
Figure 11.4
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The Initiation of Transcription

• The initiation of transcription is the most
  important stage for regulating gene expression.
• In prokaryotes and eukaryotes, regulatory
  proteins
• Bind to DNA
• Turn the transcription of genes on and off
• Unlike prokaryotic genes, transcription in
  eukaryotes is complex, involving many proteins,
  called transcription factors, that bind to DNA
  sequences called enhancers.

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Enhancers (DNA control sequences)
RNA polymerase
Bend in the DNA
Transcription
Gene
Transcription factor
Promoter
Figure 11.5
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Inhibition of Transcription

• Repressor proteins called silencers
• Bind to DNA
• Inhibit the start of transcription
• Activators are
• More typically used by eukaryotes
• Turn genes on by binding to DNA

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RNA Processing and Breakdown

• The eukaryotic cell
• Localizes transcription in the nucleus
• Processes RNA in the nucleus
• RNA processing includes the
• Addition of a cap and tail to the RNA
• Removal of any introns
• Splicing together of the remaining exons
• In alternative RNA splicing, exons may be spliced
  together in different combinations, producing
  more than one type of polypeptide from a single
  gene.

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Exons
1
4
2
3
5
DNA
4
1
2
3
5
RNA transcript
RNA splicing
or
mRNA
1
2
3
5
1
2
4
5
Figure 11.6-3
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mRNA

• Eukaryotic mRNAs
• Can last for hours to weeks to months
• Are all eventually broken down and their parts
  recycled
• Small single-stranded RNA molecules, called
  microRNAs (miRNAs), bind to complementary
  sequences on mRNA molecules in the cytoplasm, and
  some trigger the breakdown of their target mRNA.

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• The Initiation of Translation
• The process of translation offers additional
  opportunities for regulation.
• Protein Activation and Breakdown
• Post-translational control mechanisms
• Occur after translation
• Often involve cutting polypeptides into smaller,
  active final products, insulin
• The selective breakdown of proteins is another
  control mechanism operating after translation.

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Cutting
Initial polypeptide
Insulin (active hormone)
Figure 11.7-2
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Cell Signaling

• In a multicellular organism, gene regulation can
  cross cell boundaries.
• A cell can produce and secrete chemicals, such as
  hormones, that affect gene regulation in another
  cell.

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SIGNALING CELL
Secretion
Signal molecule
Plasma membrane
Reception
Receptor protein
TARGET CELL
Signal transduction pathway
Transcription factor (activated)
Nucleus
Response
Transcription
mRNA
New protein
Translation
Figure 11.8-6
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Homeotic genes

• Master control genes called homeotic genes
  regulate groups of other genes that determine
  what body parts will develop in which locations.
• Mutations in homeotic genes can produce bizarre
  effects.
• Similar homeotic genes help direct embryonic
  development in nearly every eukaryotic organism.

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Normal head
Normal fruit fly
Mutant fly with extra legs growing from head
Mutant fly with extra wings
Figure 11.9
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Fruit fly chromosome
Mouse chromosomes
Fruit fly embryo (10 hours)
Mouse embryo (12 days)
Adult fruit fly
Adult mouse
Figure 11.10
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DNA Microarrays Visualizing Gene Expression

• A DNA microarray allows visualization of gene
  expression.
• The pattern of glowing spots enables the
  researcher to determine which genes were being
  transcribed in the starting cells.
• Researchers can thus learn which genes are active
  in different tissues or in tissues from
  individuals in different states of health.

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mRNA isolated
Reverse transcriptase and fluorescently labeled
DNA nucleotides
Fluorescent cDNA
cDNA made from mRNA
DNA microarray
cDNA mixture added to wells
Unbound cDNA rinsed away
Nonfluorescent spot
Fluorescent spot
Fluorescent cDNA
DNA microarray (6,400 genes)
DNA of an expressed gene
DNA of an unexpressed gene
Figure 11.11-4
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Cloning Plants Animals The Genetic Potential
of Cells

• Differentiated cells
• All contain a complete genome
• Have the potential to express all of an
  organisms genes
• Differentiated plant cells can develop into a
  whole new organism.
• The somatic cells of a single plant can be used
  to produce hundreds of thousands of clones.
• Plant cloning
• Demonstrates that cell differentiation in plants
  does not cause irreversible changes in the DNA
• Is now used extensively in agriculture

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Single cell
Adult plant
Young plant
Cell division in culture
Root cells in growth medium
Root of carrot plant
Figure 11.12-5
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• Regeneration
• Is the regrowth of lost body parts
• Occurs, for example, in the regrowth of the legs
  of salamanders

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Reproductive Cloning of Animals

• Nuclear transplantation
• Involves replacing nuclei of egg cells with
  nuclei from differentiated cells
• Has been used to clone a variety of animals
• In 1997, Scottish researchers produced Dolly, a
  sheep, by replacing the nucleus of an egg cell
  with the nucleus of an adult somatic cell in a
  procedure called reproductive cloning, because it
  results in the birth of a new animal.

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Reproductive cloning
Donor cell
Nucleus from donor cell
Clone of donor is born
Implant embryo in surrogate mother
Therapeutic cloning
Remove nucleus from egg cell
Add somatic cell from adult donor
Grow in culture to produce an early embryo
Remove embryonic stem cells from embryo and grow
in culture
Induce stem cells to form specialized cells
for therapeutic use
Figure 11.13-5
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Figure 11.13a
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Practical Applications of Reproductive Cloning

• Other mammals have since been produced using this
  technique including
• Farm animals
• Control animals for experiments
• Rare animals in danger of extinction

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Human Cloning

• Cloning of animals
• Has heightened speculation about human cloning
• Is very difficult and inefficient
• Critics raise practical and ethical objections to
  human cloning.

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(b) Cloning for medical use
(a) The first cloned cat (right)
(c) Clones of endangered animals
Gaur
Mouflon calf with mother
Gray wolf
Banteng
Figure 11.14
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Therapeutic Cloning and Stem Cells

• The purpose of therapeutic cloning is not to
  produce a viable organism but to produce
  embryonic stem cells.
• Embryonic stem cells (ES cells)
• Are derived from blastocysts
• Can give rise to specific types of differentiated
  cells
• Adult stem cells
• Are cells in adult tissues
• Generate replacements for nondividing
  differentiated cells
• Unlike embryonic ES cells, adult stem cells
• Are partway along the road to differentiation
• Usually give rise to only a few related types of
  specialized cells

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Adult stem cells in bone marrow
Blood cells
Nerve cells
Cultured embryonic stem cells
Heart muscle cells
Different culture conditions
Different types of differentiated cells
Figure 11.15
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Umbilical Cord Blood Banking

• Umbilical cord blood
• Can be collected at birth
• Contains partially differentiated stem cells
• Has had limited success in the treatment of a few
  diseases

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Figure 11.16
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THE GENETIC BASIS OF CANCER

• In recent years, scientists have learned more
  about the genetics of cancer.
• As early as 1911, certain viruses were known to
  cause cancer.
• Oncogenes are
• Genes that cause cancer
• Found in viruses

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Oncogenes and Tumor-Suppressor Genes

• Proto-oncogenes are
• Normal genes with the potential to become
  oncogenes
• Found in many animals
• Often genes that code for growth factors,
  proteins that stimulate cell division
• For a proto-oncogene to become an oncogene, a
  mutation must occur in the cells DNA.
• Tumor-suppressor genes
• Inhibit cell division
• Prevent uncontrolled cell growth
• May be mutated and contribute to cancer

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Proto-oncogene (for protein that stimulates cell
division)
DNA
Mutation within the gene
Gene moved to new DNA position, under new controls
Multiple copies of the gene
New promoter
Oncogene
Normal growth- stimulating protein in excess
Normal growth- stimulating protein in excess
Hyperactive growth- stimulating protein
Figure 11.17
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Tumor-suppressor gene
Mutated tumor-suppressor gene
Defective, nonfunctioning protein
Normal growth- inhibiting protein
Cell division under control
Cell division not under control
(a) Normal cell growth
(b) Uncontrolled cell growth (cancer)
Figure 11.18
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The Process of Science Can Cancer Therapy Be
Personalized?

• Observations Specific mutations can lead to
  cancer.
• Question Can this knowledge be used to help
  patients with cancer?
• Hypothesis DNA sequencing technology can be used
  to test tumors and identify which cancer-causing
  mutations they carry.
• Experiment Researchers screened for 238 possible
  mutations in 1,000 human tumors from 18 different
  body tissues.
• Results
• No mutations are present in every tumor.
• Each tumor involves different mutations.
• It is possible to cheaply and accurately
  determine which mutations are present in a given
  cancer patient.

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Table 11.1
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The Progression of a Cancer

• Over 150,000 Americans will be stricken by cancer
  of the colon or rectum this year.
• Colon cancer
• Spreads gradually
• Is produced by more than one mutation
• The development of a malignant tumor is
  accompanied by a gradual accumulation of
  mutations that
• Convert proto-oncogenes to oncogenes
• Knock out tumor-suppressor genes

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Colon wall
Increased cell division
Growth of benign tumor
Growth of malignant tumor
Cellular changes
Second tumor-suppressor gene inactivated
Tumor-suppressor gene inactivated
Oncogene activated
DNA changes
Figure 11.19-3
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Chromosomes
1 mutation
4 mutations
3 mutations
2 mutations
Normal cell
Malignant cell
Figure 11.20-5
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Inherited Cancer

• Most mutations that lead to cancer arise in the
  organ where the cancer starts.
• In familial or inherited cancer
• A cancer-causing mutation occurs in a cell that
  gives rise to gametes
• The mutation is passed on from generation to
  generation
• Breast cancer
• Is usually not associated with inherited
  mutations
• In some families can be caused by inherited,
  BRCA1 cancer genes

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Cancer Risk and Prevention

• Cancer
• Is one of the leading causes of death in the
  United States
• Can be caused by carcinogens, cancer-causing
  agents found in the environment, including
• Tobacco products
• Alcohol
• Exposure to ultraviolet light from the sun
• Exposure to carcinogens
• Is often an individual choice Can be avoided
• Some studies suggest that certain substances in
  fruits and vegetables may help protect against a
  variety of cancers.

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Table 11.2
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Evolution ConnectionThe Evolution of Cancer in
the Body

• Evolution drives the growth of a tumor.
• Like individuals in a population of organisms,
  cancer cells in the body
• Have the potential to produce more offspring than
  can be supported by the environment
• Show individual variation, which
• Affects survival and reproduction
• Can be passed on to the next generation of cells

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DNA unpacking
Transcription
RNA processing
RNA transport
mRNA breakdown
Translation
Protein activation
Protein breakdown
Figure 11.UN06
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Nucleus from donor cell
Embryo implanted in surrogate mother
Clone of nucleus donor
Early embryo resulting from nuclear transplantatio
n
Figure 11.UN07
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Nucleus from donor cell
Embryonic stem cells in culture
Specialized cells
Early embryo resulting from nuclear transplantatio
n
Figure 11.UN08
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Proto-oncogene (normal)
Oncogene
Mutation
Normal protein
Mutant protein
Out-of-control growth (leading to cancer)
Normal regulation of cell cycle
Normal growth-inhibiting protein
Defective protein
Mutation
Mutated tumor-suppressor gene
Tumor-suppressor gene (normal)
Figure 11.UN09