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AP Chapter 20 Biotechnology and Genetic Engineering
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Biotechnology andGenetic Engineering
AP Biology Chapter 20
Terminology
• Genetic engineering – direct manipulation of genetic material for practical purposes
• Biotechnology – use of living organisms or their components to make products for us
• Recombinant DNA – combining pieces of DNA from different organisms
• Gene cloning – making copies of DNA
Making recombinant DNA
• Plasmids (small circular pieces of DNA in bacterial cells) are used to insert pieces of foreign DNA
The DNA is cut using restriction enzymes
What are restriction enzymes?
• Restriction enzymes come from bacteria and recognize a particular pattern of DNA, often 4, 6 or 8 base pairs long, and then cut the DNA within this recognized sequence.
• Bacteria use these enzymes to kill off other competing bacteria by cutting up their DNA.
How do they cut?
STICKY ENDS BLUNT ENDS
ACT GAA TTC CGG AAT GAA TTC
TGA CTT AAG GCC TTA CTT AAG
Where would the enzyme EcoRI cut?
ACT GAA TTC CGG AAT GAA TTC
TGA CTT AAG GCC TTA CTT AAG
There would be three pieces: one 4 bases, one 12 bases, and one 5 bases.
Making recombinant DNA in plasmids
The collection of thousands of clones of bacteria containing recombinant plasmids is called a genomic library.
Genes can be cloned into
vectors such as plasmids
Fig. 20-2
DNA of chromosome
Cell containing geneof interest
Gene inserted intoplasmid
Plasmid put intobacterial cell
RecombinantDNA (plasmid)
Recombinantbacterium
Bacterialchromosome
Bacterium
Gene ofinterest
Host cell grown in cultureto form a clone of cellscontaining the “cloned”gene of interest
Plasmid
Gene ofInterest
Protein expressedby gene of interest
Basic research andvarious applications
Copies of gene Protein harvested
Basicresearchon gene
Basicresearchon protein
Gene for pest resistance inserted into plants
Gene used to alter bacteria for cleaning up toxic waste
Protein dissolvesblood clots in heartattack therapy
Human growth hor-mone treats stuntedgrowth
2
4
1
3
Fig. 20-2a
DNA of chromosome
Cell containing geneof interest
Gene inserted intoplasmid
Plasmid put intobacterial cell
RecombinantDNA (plasmid)
Recombinantbacterium
Bacterialchromosome
Bacterium
Gene ofinterest
Plasmid
2
1
2
Fig. 20-2b
Host cell grown in cultureto form a clone of cellscontaining the “cloned”gene of interest
Gene ofInterest
Protein expressedby gene of interest
Basic research andvarious applications
Copies of gene Protein harvested
Basicresearchon gene
Basicresearchon protein
4
Recombinantbacterium
Gene for pest resistance inserted into plants
Gene used to alter bacteria for cleaning up toxic waste
Protein dissolvesblood clots in heartattack therapy
Human growth hor-mone treats stuntedgrowth
3
Steps
1. Plasmid and human DNA are isolated.
2. Both DNAs are cut with the same restriction enzyme.
3. “new” DNA is ligated into plasmid
4. Recombinant plasmids are inserted into bacterial cells.
5. Plate bacteria on agar. Bacteria will express new genes.
Nucleic Acid Hybridization
• Used to detect genes
• The DNA of the cell is denatured to produce single stranded DNA.
• The radioactive probe will hybridize (bond) with complementary bases if present.
• Probes can be radioactive isotopes or
flourescent dyes.
The radioactive probe is made by determining a short segment of the protein sequence, then "back translating" to the possible DNA sequences. Short DNA sequences are synthesized to match the protein sequence. Then these DNA oligomers (known as "oligos") are radiolabeled, and applied to the blotted clones. They should hybridize only to clones containing sequence encoding the desired protein.
Expression of eukaryoticgenes in prokaryotes
• Use an expression vector with a prokaryotic promoter upstream from the location of the gene.
• Create artificial genes without introns since bacteria do not have the machinery for eliminating introns.
• YACS
What are YACS?
• Yeast artificial chromosomes that carry foreign DNA.
• Yeast cells have plasmids that can act as vectors.
Electroporation
• injecting DNA into eukaryotic cells
PCR Polymerase Chain Reaction
• Used to amplify DNA
• Discovered by Kary Mullis (GT grad)
A Thermocycler
Steps of PCR?
• Denature DNA (94-96 C)
• Anneal (base pair) primers (50 – 65 C)
• Extend primers (72 for polymerase to work)
• Machines called thermocyclers do this.
http://www.dnalc.org/ddnalc/resources/shockwave/pcranwhole.html
• In PCR, a heat-stable DNA polymerase is used, most commonly Taq Polymerase from the thermophilic microbe Thermus aquaticus. Thomas Brock discovered T. aquaticus from a hot spring at Yellowstone National Park.
Why is PCR used prior to cloning a gene in cells?
The task of later identifying the clone carrying the gene is simplified.
Applications of PCR
PCR has replaced cloning for many purposes, particularly the sequencing of DNA.
• It is faster and requires no vectors, which can mutate as they reproduce.
• It can be used forensically, to amplify tiny amounts of DNA from criminal evidence; or clinically, to detect DNA sequences linked to inherited disorders.
What is gel electrophoresis?
• A technique to separate DNA based on the movement of DNA fragments from neg to pos (DNA is neg).
• Smaller fragments travel farther.
• Samples are placed in gels.
Gel Electrophoresis
Southern BlottingDNA Fingerprinting
1. Isolate DNA2.Cut DNA into fragments with restriction enzymes.3.Electrophorese.4.Blot onto nylon membrane.5.Apply radioactive probes.6.Wash to remove unbonded probes.7.X-Ray.
Southern Blotting
Sanger Sequencing
• Used to sequence short segments of DNA
• Fragments are incubated with fluorescent dyes.
• When fragments hybridize with the tagged nucleotide, the hybridization stops.
• Fragments are electrophoresed and analyzed.
Early DNA Sequencing
Analyzing Expression of Genes
• Northern Blotting, in situ hybridization – using radioactive probes to look for mRNA being produced
• RT-PCR – Reverse transcriptase-polylmerase chain reaction – makes cDNA from mRNAs and then PCRs the DNA for electrophoresis
• Micro – arrays - Isolate mRNA from cells, make cDNA using reverse transcriptase, then uses cDNA to explore collections of genomic DNA
• Microarrays are useful in discerning gene expression in different tissues AND at different stages of development.
• Different brightness and
colors signify rates of
expression.
Determining Gene Function
• In vitro mutagenesis – changes made to cloned gene, gene returned to cell and it “knocks out” the normal gene. Then look for abnormalities.
• RNA interference (RNAi) – uses double RNA to block translation of mRNA.
Cloning Organisms
• Organismal cloning – producing genetically identical individuals from a single somatic cell of a multicellular organism
In plants• Steward demonstrated
genomic equivalence in plants by growing carrot plants from differentiated root cells.
• Most plant cells remain totipotent, retaining the ability to give rise to a complete new organisms.
In Animals
• Briggs and all transplanted nuclei from embryonic frog cells into enucleated egg cells and produced cloned frogs
• Nuclear transplantation – name of process
• Whether normal development occurred depended on developmental age of the transplanted nucleus.
Fig. 20-17
EXPERIMENT
Less differ-entiated cell
RESULTS
Frog embryo Frog egg cell
UV
Donornucleustrans-planted
Frog tadpole
Enucleated egg cell
Egg with donor nucleus activated to begin
development
Fully differ-entiated(intestinal) cell
Donor nucleus trans-planted
Most developinto tadpoles
Most stop developingbefore tadpole stage
Nuclear Transplantation
And then Dolly came along in 1997
Fig. 20-18
TECHNIQUE
Mammarycell donor
RESULTS
Surrogatemother
Nucleus frommammary cell
Culturedmammary cells
Implantedin uterusof a thirdsheep
Early embryo
Nucleusremoved
Egg celldonor
Embryonicdevelopment Lamb (“Dolly”)
genetically identical tomammary cell donor
Egg cellfrom ovary
Cells fused
Grown inculture
1
33
4
5
6
2
Why Dolly died young 6 yrs
• Dolly's telomeres were found to be approximately 80% of the length they should be for a sheep her age.
• Also there is the concern of damaged DNA being carried into the clone
Cloned animals do not look exactly like the transplanted nucleus due to cytoplasmic affects.
RainbowCC
CC and her Surrogate mom
• In most nuclear transplantation studies, only a small percentage of cloned embryos have developed normally to birth
• Many epigenetic changes, such as acetylation of histones or methylation of DNA, must be reversed in the nucleus from a donor animal in order for genes to be expressed or repressed appropriately for early stages of development
Stem Cells
• Relatively unspecialized cells that continue to reproduce themselves and can be induced to form specialized cells
• Embryonic cells are more totipotent than adult stem cells
• Therapeutic cloning – using stem cells to replace organs and tissues
• Reproductive cloning – using stem cells to reproduce new organisms
• Both raise ethical
debates
Benefits of DNA technology
• Medical Applications
• identification of human genes in which mutation plays a role in genetic diseases
• Single nucleotide polymorphisms (SNPs) are useful genetic markers
• These are single base-pair sites that vary in a population
• When a restriction enzyme is added, SNPs result in DNA fragments with different lengths, or restriction fragment length polymorphisms (RFLP)
Fig. 20-21
Disease-causingallele
DNA
SNP
Normal alleleT
C
Human Gene Therapy
• Gene therapy is the alteration of an afflicted individual’s genes
• Vectors, such as viruses, are used for delivery of genes into specific types of cells, for example bone marrow
• It may be difficult to target cells.• Gene therapy raises ethical questions,
such as whether human germ-line cells should be treated to correct the defect in future generations
Fig. 20-22
Bonemarrow
Clonedgene
Bonemarrowcell frompatient
Insert RNA version of normal alleleinto retrovirus.
Retroviruscapsid
Viral RNA
Let retrovirus infect bone marrow cellsthat have been removed from thepatient and cultured.
Viral DNA carrying the normalallele inserts into chromosome.
Inject engineeredcells into patient.
1
2
3
4
Pharmaceutical Products
• Advances in DNA technology and genetic research are important to the development of new drugs to treat diseases
• In particular “pharm” animals and plants can be used to produce certain products
Fig. 20-23
Forensic Evidence and Genetic Profiles
• An individual’s unique DNA sequence, or genetic profile, can be obtained by analysis of tissue or body fluids
• Even more sensitive is the use of genetic markers called short tandem repeats (STRs), which are variations in the number of repeats of specific DNA sequences
Fig. 20-24This photo shows EarlWashington just before his release in 2001,after 17 years in prison.
These and other STR data exonerated Washington andled Tinsley to plead guilty to the murder.
(a)
Semen on victim
Earl Washington
Source of sample
Kenneth Tinsley
STRmarker 1
STRmarker 2
STRmarker 3
(b)
17, 19
16, 18
17, 19
13, 16 12, 12
14, 15 11, 12
13, 16 12, 12
Environmental Cleanup
• Some modified microorganisms can be used to extract minerals from the environment or degrade potentially toxic waste materials
• Biofuels make use of crops such as corn, soybeans, and cassava to replace fossil fuels
Genetic Engineering in Plants
• Agricultural scientists have endowed a number of crop plants with genes for desirable traits
• The Ti plasmid is the most commonly used vector for introducing new genes into plant cells
• Most public concern about possible hazards centers on genetically modified (GM) organisms used as food
• Some are concerned about the creation of “super weeds” from the transfer of genes from GM crops to their wild relatives
Fig. 20-25
Site whererestrictionenzyme cuts
T DNA
Plant with new trait
Tiplasmid
Agrobacterium tumefaciens
DNA withthe geneof interest
RecombinantTi plasmid
TECHNIQUE
RESULTS