Download AP Ch 19

WHAT PRACTICAL
USES HAS OUR
KNOWLEDGE OF
GENETICS
PROVIDED?
VIDEO(S)
Genetics, longevity, and computer science
AP Ch 20
Biotechnology and genetic engineering
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• Biotechnology – use of organisms’ genes and
current technology to advance society
• Genetic Engineering – manipulation of genes for
practical purpose
• Genomics – study of genomes and proteins
(proteomics)
– Genomics is HOT
• Now lets explore some DNA manipulation and
usage lab techniques
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General Applications of DNA technology
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General Applications of DNA technology
• Diagnosis of diseases
• Gene therapy
• Forensics: matching crime scene DNA to
suspects and victims
• Genetic engineering of food/animals:
– adding traits of other organisms to hosts
– Removing, modifying, or enhancing pre-existing
genes
– Inserting designer genes into organism (e.g.
antibiotic production in corn)
•
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http://www.pbs.org/wgbh/nova/genome/program.html# (long vid)
6
Key tools of the trade:
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Key tools of the trade:
• Restriction enzymes – protective enzymes
from bacteria are used to cut other DNA
segments at specific locations
• often used to make plasmids with genes of
interest, p 398
• Vectors – delivers chosen gene into a host cell
where it will be replicated (e.g. bacterial
plasmid, virus)
• Electroporation, microscopic needles, and
bullets can also introduce foreign DNA into
host
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Restriction
enzymes
in use
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Microtiter plates with 96, 384 and 1536
wells (often called “96-well plate”). How helpful?
Probes – piece of single-stranded DNA or RNA of a known gene (p. 400)
•
•
used to find a specific DNA sequence by hybridization
Probe can be traced because it is labeled with a glowing isotope
Genomic libraries – genetic “library” of
an organism’s DNA, over 1000 completed
– Can be genomic libraries or complementary DNA
(cDNA made in reverse transcription from mRNA)
• What would an advantage of having an entire genome on
file have over cDNA?
– Human Genome Project - (accomplished 2001)
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Genomic libraries – genetic “library” of
an organism’s DNA, over 1000 completed
– Can be genomic libraries or complementary DNA
(cDNA made in reverse transcription from mRNA)
• What would an advantage of having an entire
genome on file have over cDNA?
– Human Genome Project - (accomplished 2001)
• What would be next step to make this knowledge
useful?
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Genomic libraries – genetic “library” of
an organism’s DNA, over 1000 completed
– Can be genomic libraries or complementary DNA
(cDNA made in reverse transcription from mRNA)
• What would an advantage of having an entire
genome on file have over cDNA?
– Human Genome Project - (accomplished 2001)
• What would be next step to make this knowledge
useful?
• How would they acquire such knowledge?
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DNA techniques:
• PCR- see diagram to right, make
copies of chosen of
DNA segments
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DNA techniques:
• PCR- see diagram to right, make
copies of chosen of DNA
segments
– How long until you have 100
DNA copies? 1 billion?
• Gel electrophoresis see diagram
next pg., separates DNA based
on size,
– moves by electric charge as
DNA is -,
– Used for DNA “fingerprinting”
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Gene Cloning: producing copies of chosen gene
• Benefits: 1. amplifying a chosen gene
• 2. produce a chosen protein product
Give an example of #2
for practical purpose
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Practical
uses of cloned
genes,
including
cellular
transformation
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Use of restriction
sites on DNA
segment in gel
electrophoresis
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A technique called Southern blotting combines gel electrophoresis of
DNA fragments with nucleic acid hybridization
Specific DNA fragments can be identified by Southern blotting, using
labeled probes that hybridize to the DNA immobilized on a “blot” of gel
Figure 20.13
TECHNIQUE
1 cDNA synthesis
mRNAs
cDNAs
2 PCR amplification
Primers
-globin
gene
3 Gel electrophoresis
RESULTS
Reverse PCR: compares
gene expression between
samples (such as 6 stages
of organismal development)
Embryonic stages
1 2 3 4 5 6
Microarrays:
tests thousands of
genes in tissue
under different
environmental
conditions
•Can reveal profiles of
genes over a lifetime of
an organism
•How can this technique
be used for medical
discovery?
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• Real-time PCR
– (or quantitative PCR, a.k.a. Q-PCR)
simultaneously amplifies and quantifies
segments of DNA
Use of entire genome in
biotechnology
• Cloning
• Stem cells
Whole–
organism
cloning:
Done by
nuclear
transfer
How is this
useful?
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Stem cells
• Unspecialized cells that can reproduce
indefinitely and under can become other
types of specialized cells?
– What would determine the type of cell a stem
cell becomes?
• Can be multipotent, pluripotent,
omnipotent stem cells
Figure 20.21
Embryonic
stem cells
Adult
stem cells
Cells generating
some cell types
Cells generating
all embryonic
cell types
Cultured
stem cells
Different
culture
conditions
Different
types of
differentiated
cells
Liver
cells
Nerve
cells
Blood
cells
Figure 20.22
1 Remove skin cells
from patient.
2 Reprogram skin cells
so the cells become
induced pluripotent
stem (iPS) cells.
Patient with
damaged heart
tissue or other
disease
3 Treat iPS cells so
that they differentiate
into a specific
cell type.
4 Return cells to
patient, where
they can repair
damaged tissue.
FigureCloned
20.23 gene
Gene Therapy
1 Insert RNA version of normal allele
into retrovirus.
Viral RNA
Retrovirus
capsid
2 Let retrovirus infect bone marrow cells
that have been removed from the
patient and cultured.
3 Viral DNA carrying the normal
allele inserts into chromosome.
Bone
marrow
cell from
patient
4 Inject engineered
cells into patient.
Bone
marrow
Protein Production by “Pharm” Animals
• Transgenic animals are made by introducing
genes from one species into the genome of
another animal
– Transgenic animals can be pharmaceutical “factories,”
producers of large amounts of otherwise rare
substances for various uses (medical, nourishment)
© 2011 Pearson Education, Inc.
Figure 20.24
Do you
consume
genetically
modified
foods?
Modification
Percent
Mod
ified
in
US
Resistant to
herbicides
Herbicide resistant gene taken
from bacteria inserted
into soybean
93%
77%
Resistant to
herbicides and
insects.
Vitaminenriched corn
New genes, some from the
bacterium
added/transferred into
plant genome.
86%
26%
Cotton
(cotto
nseed
oil)
Pest-resistant cotton
Bt crystal protein gene
added/transferred into
plant genome
93%
49%
Alfalfa
Resistant to
herbicides
New genes added/transferred
into plant genome.
Food
Soybeans
Corn,
Tomatoes
Properties of the
genetically
modified
variety
enzyme (PG) is
suppressed,
retarding fruit
softening after
harvesting.
RNAi of PG enzyme added
into plant genome
Percent
Modifi
ed in
world
Planted 200507,
unban
ned
1/2011
Failed
comme
rcially
in US
Small
quantiti
es
grown
in
China
More examples
Food
Properties of the
genetically
modified
variety
Modification
Percent
Mod
ified
in
US
New genes added/transferred
into plant genome
95%
Sugar
beet
Resistance to
herbicides
Golden
Rice
contain betacarotene (a
source of
vitamin A)
contain gene from daffodils
and from a bacterium
Resistance to yellow
mosaic viruses
Contains coat protein genes
of viruses.
Zucchini
on the
mark
et in
2013
13%
Percent
Modifi
ed in
world
9%
Is genetically modified food (GM)
safe?
Why or why not?
AP Ch 21
Genomes and Their Evolution
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36
• Genomics is the study of whole sets of genes
and their interactions
• Bioinformatics is the application of
computational methods to the storage and
analysis of biological data
© 2011 Pearson Education, Inc.
What genomic information distinguishes a human from a chimpanzee?
Concept 21.1: New approaches have
accelerated the pace of genome
sequencing
• The most ambitious mapping project to date has
been the sequencing of the human genome
• Officially begun as the Human Genome Project
in 1990, the sequencing was largely completed
by 2003
• The project had three stages
– Genetic (or linkage) mapping
– Physical mapping
– DNA sequencing
© 2011 Pearson Education, Inc.
Three-Stage Approach to Genome
Sequencing
• Step 1: A linkage map (genetic map) maps the
location of several thousand genetic markers on
each chromosome
– Recombination frequencies are used to determine the
order and relative distances between genetic markers
© 2011 Pearson Education, Inc.
Three-stage approach to sequencing an entire genome.
Chromosome
bands
Cytogenetic map
Genes located
by FISH
1 Linkage mapping
Genetic
markers
2 Physical mapping
Overlapping
fragments
3 DNA sequencing
Whole-Genome Shotgun Approach to
Genome Sequencing
• The whole-genome shotgun approach was
developed by J. Craig Venter in 1992
• This approach skips genetic and physical mapping
and sequences random DNA fragments directly
– Powerful computer programs are used to order
fragments into a continuous sequence
© 2011 Pearson Education, Inc.
Figure 21.3-1
1 Cut the DNA into
overlapping fragments short enough
for sequencing.
2 Clone the fragments
in plasmid or phage
vectors.
Figure 21.3-2
1 Cut the DNA into
overlapping fragments short enough
for sequencing.
2 Clone the fragments
in plasmid or phage
vectors.
3 Sequence each
fragment.
Figure 21.3-3
1 Cut the DNA into
overlapping fragments short enough
for sequencing.
2 Clone the fragments
in plasmid or phage
vectors.
3 Sequence each
fragment.
4 Order the
sequences into
one overall
sequence
with computer
software.
• Both the three-stage process and the wholegenome shotgun approach were used for the
Human Genome Project and for genome
sequencing of other organisms
– A complete haploid
consists of 3.2
© 2011 Pearson Education, Inc.
set of human chromosomes
billion base pairs
• Technological advances have also facilitated
metagenomics, in which DNA from a group of
species (a metagenome) is collected from an
environmental sample and sequenced
© 2011 Pearson Education, Inc.
Concept 21.2 Scientists use
bioinformatics to analyze genomes and
their functions
• The Human Genome Project established
databases to make data available on the Internet
• Bioinformatics resources are provided by:
– National Library of Medicine and the National
Institutes of Health (NIH) created the National Center
for Biotechnology Information (NCBI)
– European Molecular Biology Laboratory
– DNA Data Bank of Japan
– BGI in Shenzhen, China
© 2011 Pearson Education, Inc.
NCBI database – can compare DNA, RNA, or even proteins
Understanding Genes and Gene
Expression at the Systems Level
• Proteomics is the systematic study of all proteins
encoded by a genome
© 2011 Pearson Education, Inc.
The systems biology approach to protein interactions
Glutamate
biosynthesis
Translation and
ribosomal functions
Mitochondrial
functions
Vesicle
fusion
RNA processing
Peroxisomal
functions
Transcription
and chromatinrelated functions
Metabolism
and amino acid
biosynthesis
Nuclearcytoplasmic
transport
Secretion
and vesicle
transport
Nuclear migration
and protein
degradation
Mitosis
DNA replication
and repair
Cell polarity and
morphogenesis
Protein folding,
glycosylation, and
cell wall biosynthesis
Serinerelated
biosynthesis
Amino acid
permease pathway
Application of Systems Biology to
Medicine
• A systems biology approach has several medical
applications
– The Cancer Genome Atlas project is currently
seeking all the common mutations in 13 types of
cancer by comparing gene sequences and
expression in cancer versus normal cells
© 2011 Pearson Education, Inc.
Silicon and glass “chips” have been produced that hold a
microarray of most known human genes
The expression of all/most genes at the same time.
What are the pros/cons of evaluating someone’s entire genome?
Table 21.1
What stands
out to you from
these data?
Exons (1.5%)
Introns (5%)
Types of DNA
sequences in the
human genome
Regulatory
sequences
(20%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
L1
sequences
(17%)
Alu elements
(10%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(14%)
Simple sequence
DNA (3%)
Large-segment
duplications (56%)
Intergenic DNA is noncoding and found between genes
– Pseudogenes are former genes that have
accumulated mutations and are nonfunctional
– Repetitive DNA is present in multiple copies in the
genome
•
About three-fourths of repetitive DNA is made up of transposable
elements (a.k.a. jumping genes) and sequences related to them
© 2011 Pearson Education, Inc.
Figure 21.8
Barbara McClintock and transposable DNA
Types of transposable elements:
• Eukaryotic transposable elements are of two
types
– Transposons, which move by means of a DNA
intermediate
– Retrotransposons, which move by means of an
RNA intermediate
© 2011 Pearson Education, Inc.
Figure 21.9
Transposon
DNA of
genome
Transposon
is copied
Mobile transposon
New copy of
transposon
Insertion
Figure 21.10
Retrotransposon
New copy of
retrotransposon
Formation of a
single-stranded
RNA intermediate
RNA
Insertion
Reverse
transcriptase
Gene Families
DNA
RNA transcripts
Nontranscribed
Transcription unit
spacer
-Globin
-Globin
Heme
DNA
18S
5.8S
28S
rRNA
28S
5.8S
18S
(a) Part of the ribosomal RNA gene family
-Globin gene family
Chromosome 16

Embryo
   2 1 
2
1
-Globin gene family
Chromosome 11

G
A
Fetus
and adult Embryo Fetus



Adult
(b) The human -globin and -globin gene families
Alterations of Chromosome Structure: Humans have 23 pairs
of chromosomes, while chimpanzees have 24 pairs……How?
Human
chromosome 2
Chimpanzee
chromosomes
Telomere
sequences
Centromere
sequences
Telomere-like
sequences
12
Human
chromosome 16
Centromere-like
sequences
13
(a) Human and chimpanzee chromosomes
Mouse
chromosomes
7
8
(b) Human and mouse chromosomes
16
17
Alterations of Chromosome Structure: Humans have 23 pairs
of chromosomes, while chimpanzees have 24 pairs……How?
Human
chromosome 2
Chimpanzee
chromosomes
Telomere
sequences
Centromere
sequences
Telomere-like
sequences
12
Human
chromosome 16
Centromere-like
sequences
13
(a) Human and chimpanzee chromosomes
Mouse
chromosomes
7
8
(b) Human and mouse chromosomes
16
17
• The rate of duplications and inversions seems to
have accelerated about 100 million years ago
–WHY?
© 2011 Pearson Education, Inc.
• The rate of duplications and
inversions seems to have
accelerated about 100 million
years ago
– This coincides with when large
dinosaurs went extinct and
mammals diversified
• Chromosomal rearrangements
are thought to contribute to the
generation of new species
– We still have recombination “hot
spots” now. What types of traits
are being selected for now
intensively?
© 2011 Pearson Education, Inc.
Transposable elements can
provide sites for crossover
between nonsister chromatids
Incorrect pairing
of two homologs
during meiosis
Nonsister
Gene
chromatids
Crossover
point
and
Transposable
element
How do Transposable Elements
Contribute to Genome Evolution?
© 2011 Pearson Education, Inc.
How Transposable Elements Contribute
to Genome Evolution
1. may facilitate crossing over between different
chromosomes
2. Insertion of transposable elements within a
protein-coding sequence may block protein
production
3. Insertion of transposable elements within a
regulatory sequence may increase or
decrease protein production
– changes are usually detrimental but may on occasion
prove advantageous to an organism
© 2011 Pearson Education, Inc.
Concept 21.6: Comparing genome
sequences provides clues to evolution
and development
© 2011 Pearson Education, Inc.
Figure 21.16
Bacteria
Most recent
common
ancestor
of all living
things
Eukarya
Archaea
4
1
3
2
Billions of years ago
0
Chimpanzee
Human
Mouse
70
60
50
40
30
20
Millions of years ago
10
0
Comparing Distantly Related Species
• Highly conserved genes have changed very little
over time
• These help clarify relationships among species
that diverged from each other long ago
© 2011 Pearson Education, Inc.
• Human and chimpanzee genomes differ by
1.2% at single base-pairs
– Several genes are evolving faster in humans
than chimpanzees
– Which do you think these would control?
© 2011 Pearson Education, Inc.
• Human and chimpanzee genomes differ by
1.2% at single base-pairs
– Several genes are evolving faster in humans
than chimpanzees
– These include genes involved in defense
against malaria and tuberculosis and in
regulation of brain size, and genes that code
for transcription factors
© 2011 Pearson Education, Inc.
Comparing Genomes Within a Species
• As a species, humans have only been around
about 200,000 years and have low withinspecies genetic variation
• Variation within humans is due to single nucleotide
polymorphisms, inversions, deletions, and duplications
© 2011 Pearson Education, Inc.
Comparing Developmental Processes
• Evolutionary developmental
biology, or evo-devo, is the study
of the evolution of developmental
processes in multicellular
organisms
– Genomic information shows that
minor differences in gene sequence
or regulation can result in striking
differences in form
© 2011 Pearson Education, Inc.
Widespread Conservation of Developmental
Genes Among Animals
• Molecular analysis of the homeotic genes in
Drosophila has shown that they all include a
sequence called a homeobox
– An identical or very similar nucleotide sequence has
been discovered in the homeotic genes of both
vertebrates and invertebrates
– Homeotic genes in animals are called Hox genes
© 2011 Pearson Education, Inc.
review
Adult
fruit fly
Fruit fly embryo
(10 hours)
Fly chromosome
Mouse
chromosomes
Mouse embryo
(12 days)
Adult mouse
Thorax
Genital
segments
Abdomen
Differences in Hox
genes influences
body plan.
Artemia has
coexpression in
the thorax region.
Thorax
Abdomen
Summary: Genomes vary in size, number of genes, and density
Bacteria
Genome
size
Number of
genes
Gene
density
Introns
Other
noncoding
DNA
Archaea
Most are 16 Mb
1,5007,500
Higher than in eukaryotes
None in
protein-coding
genes
Present in
some genes
Very little
Eukarya
Most are 104,000 Mb, but a
few are much larger
5,00040,000
Lower than in prokaryotes
(Within eukaryotes, lower
density is correlated with larger
genomes.)
Unicellular eukaryotes:
present, but prevalent only in
some species
Multicellular eukaryotes:
present in most genes
Can be large amounts;
generally more repetitive
noncoding DNA in
multicellular eukaryotes