Download Chapter 20: Biotechnology

Chapter 20:
Biotechnology
Ms. Whipple
Brethren Christian High School
1. What is Recombinant DNA?
• Recombinant DNA are nucleotide sequences from two
different sources, often two species, are combined in vitro
into the same DNA molecule
• Methods for making recombinant DNA are central to
genetic engineering, the direct manipulation of genes
for practical purposes
2. What is Biotechnology and Genetic Engineering? How is
Genetic Engineering advancing our society? Give me two
examples of genetic engineering not found in the book.
• Genetic Engineering is the direct manipulation of genes for
practical purposes
• DNA technology has revolutionized Biotechnology, the
manipulation of organisms or their genetic components to make
useful products
• An example of DNA technology is the microarray, a
measurement of gene expression of thousands of different genes
3. How are Bacteria and Plasmids used for
cloning?
• Most methods for cloning pieces of DNA in the laboratory
share general features, such as the use of bacteria and their
plasmids
• Plasmids are small circular DNA molecules that replicate
separately from the bacterial chromosome
• Cloned genes are useful for making copies of a particular
gene and/or producing a protein product
3. How are Bacteria and Plasmids used for
cloning?
• Gene cloning involves using bacteria to make multiple copies of a
gene
• Foreign DNA is inserted into a plasmid, and the recombinant
plasmid is inserted into a bacterial cell
• Reproduction in the bacterial cell results in cloning of the plasmid
including the foreign DNA
• This results in the production of multiple copies of a single gene
Fig. 20-2a
Cell containing gene
of interest
Bacterium
1 Gene inserted into
plasmid
Bacterial
chromosome
Plasmid
Recombinant
DNA (plasmid)
Gene of
interest
2
2 Plasmid put into
bacterial cell
Recombinant
bacterium
DNA of
chromosome
Fig. 20-2b
Recombinant
bacterium
3 Host cell grown in culture
to form a clone of cells
containing the “cloned”
gene of interest
Protein expressed
by gene of interest
Gene of
Interest
Copies of gene
Protein harvested
4 Basic research and
Basic
research
on gene
Gene for pest
resistance inserted
into plants
various applications
Gene used to alter
bacteria for cleaning
up toxic waste
Protein dissolves
blood clots in heart
attack therapy
Basic
research
on protein
Human growth hormone treats stunted
growth
4. Gene cloning may be used for which two
purposes? Give me an example of each.
• Gene cloning is used to make many copies of
a gene for research (such as a disease gene)
and study or used to make a protein product
(such as insulin).
5. How are Restriction Enzymes used for creating Recombinant
DNA? Please use the words Restriction Site, Restriction Fragments,
Sticky End, and DNA ligase in your answer.
• Bacterial restriction enzymes cut DNA molecules at specific DNA
sequences called restriction sites
• A restriction enzyme usually makes many cuts, yielding restriction
fragments
• The most useful restriction enzymes cut DNA in a staggered way, producing
fragments with “sticky ends” that bond with complementary sticky ends of
other fragments
• DNA ligase is an enzyme that seals the bonds between restriction fragments
Fig. 20-3-1
Restriction site
DNA
1
5
3
3
5
Restriction enzyme
cuts sugar-phosphate
backbones.
Sticky end
Fig. 20-3-2
Restriction site
DNA
1
5
3
3
5
Restriction enzyme
cuts sugar-phosphate
backbones.
Sticky end
2
DNA fragment added
from another molecule
cut by same enzyme.
Base pairing occurs.
One possible combination
Fig. 20-3-3
Restriction site
DNA
1
5
3
3
5
Restriction enzyme
cuts sugar-phosphate
backbones.
Sticky end
2
DNA fragment added
from another molecule
cut by same enzyme.
Base pairing occurs.
One possible combination
3
DNA ligase
seals strands.
Recombinant DNA molecule
6. Briefly describe the steps for gene cloning
the B-Globin gene in Hummingbirds.
• Several steps are required to clone the hummingbird β-globin gene in a
bacterial plasmid:
•
•
•
•
•
•
•
The hummingbird genomic DNA and a bacterial plasmid are isolated
Both are digested with the same restriction enzyme
The fragments are mixed, and DNA ligase is added to bond the fragment sticky ends
Some recombinant plasmids now contain hummingbird DNA
The DNA mixture is added to bacteria that have been genetically engineered to accept it
The bacteria are plated on a type of agar that selects for the bacteria with recombinant plasmids
This results in the cloning of many hummingbird DNA fragments, including the
β-globin gene
Fig. 20-4-1
Hummingbird
cell
TECHNIQUE
Bacterial cell
lacZ gene
Restriction
site
ampR gene
Bacterial
plasmid
Sticky
ends
Gene of interest
Hummingbird
DNA fragments
Fig. 20-4-2
Hummingbird
cell
TECHNIQUE
Bacterial cell
lacZ gene
Restriction
site
ampR gene
Sticky
ends
Bacterial
plasmid
Gene of interest
Hummingbird
DNA fragments
Nonrecombinant
plasmid
Recombinant plasmids
Fig. 20-4-3
Hummingbird
cell
TECHNIQUE
Bacterial cell
lacZ gene
Restriction
site
ampR gene
Sticky
ends
Bacterial
plasmid
Gene of interest
Hummingbird
DNA fragments
Nonrecombinant
plasmid
Recombinant plasmids
Bacteria carrying
plasmids
Fig. 20-4-4
Hummingbird
cell
TECHNIQUE
Bacterial cell
lacZ gene
Restriction
site
ampR gene
Sticky
ends
Bacterial
plasmid
Gene of interest
Hummingbird
DNA fragments
Nonrecombinant
plasmid
Recombinant plasmids
Bacteria carrying
plasmids
RESULTS
Colony carrying nonrecombinant plasmid
with intact lacZ gene
Colony carrying recombinant
plasmid with disrupted lacZ gene
One of many
bacterial
clones
7. What is the Genomic Library? How is this
used in research?
• A genomic library that is made using bacteria is the
collection of recombinant vector clones produced by
cloning DNA fragments from an entire genome
• A genomic library that is made using bacteriophages is
stored as a collection of phage clones
Fig. 20-5a
Foreign genome
cut up with
restriction
enzyme
or
Recombinant
phage DNA
Bacterial
clones
(a) Plasmid library
Recombinant
plasmids
(b) Phage library
Phage
clones
8. What is a Bacterial Artificial Chromosome? What
is the advantage of using this for research?
• A bacterial artificial chromosome (BAC) is a
large plasmid that has been trimmed down and can
carry a large DNA insert
• BACs are another type of vector used in DNA
library construction
Fig. 20-5b
Large plasmid
Large insert
with many genes
BAC
clone
(c) A library of bacterial artificial
chromosome (BAC) clones
1. What is PCR? What is it used for?
• The polymerase chain reaction, PCR, can produce many copies of a
specific target segment of DNA
• A three-step cycle—heating, cooling, and replication—brings about a chain
reaction that produces an exponentially growing population of identical
DNA molecules
• This is a very useful method if the DNA source is very limited or impure as
it can make many many copies of one segment in a short amount of time.
Fig. 20-8a
5
TECHNIQUE
3
Target
sequence
Genomic DNA
3
5
Fig. 20-8b
1 Denaturation
5
3
3
5
2 Annealing
Cycle 1
yields
2
molecules
Primers
3 Extension
New
nucleotides
Fig. 20-8c
Cycle 2
yields
4
molecules
Fig. 20-8d
Cycle 3
yields 8
molecules;
2 molecules
(in white
boxes)
match target
sequence
2. What is Gel Electrophoresis? How is it used
for research?
•
•
•
•
•
One indirect method of rapidly analyzing and comparing genomes is gel electrophoresis
This technique uses a gel as a molecular sieve to separate nucleic acids or proteins by size
A current is applied that causes charged molecules to move through the gel
Molecules are sorted into “bands” by their size
In restriction fragment analysis, DNA fragments produced by restriction enzyme digestion of a
DNA molecule are sorted by gel electrophoresis
• Restriction fragment analysis is useful for comparing two different DNA molecules, such as
two alleles for a gene
• The procedure is also used to prepare pure samples of individual fragments
Fig. 20-9a
TECHNIQUE
Mixture of
DNA molecules of
different
sizes
Power
source
– Cathode
Anode +
Gel
1
Power
source
–
+
Longer
molecules
2
Shorter
molecules
Fig. 20-9b
RESULTS
Fig. 20-10
Normal -globin allele
175 bp
DdeI
Sickle-cell
allele
Large fragment
201 bp
DdeI
Normal
allele
DdeI
DdeI
Large
fragment
Sickle-cell mutant -globin allele
376 bp
DdeI
201 bp
175 bp
Large fragment
376 bp
DdeI
DdeI
(a) DdeI restriction sites in normal and
sickle-cell alleles of -globin gene
(b) Electrophoresis of restriction fragments
from normal and sickle-cell alleles
3. Briefly describe the Southern blotting
method? What is this used for?
• 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
Fig. 20-11a
TECHNIQUE
DNA + restriction enzyme
Restriction
fragments
I
II III
Nitrocellulose
membrane (blot)
Heavy
weight
Gel
Sponge
I Normal
-globin
allele
II Sickle-cell III Heterozygote
allele
1 Preparation of restriction fragments
Alkaline
solution
2 Gel electrophoresis
Paper
towels
3 DNA transfer (blotting)
Fig. 20-11b
Radioactively labeled
probe for -globin gene
I
II III
Probe base-pairs
with fragments
Fragment from
sickle-cell
-globin allele
Fragment from
normal -globin
Nitrocellulose blot
allele
4 Hybridization with radioactive probe
I
II III
Film
over
blot
5 Probe detection
4. What two methods can be used to study gene changes in
embryonic development? Briefly describe them?
• Changes in the expression of a gene during embryonic development can be tested using
• Northern blotting combines gel electrophoresis of mRNA followed by
hybridization with a probe on a membrane
• Identification of mRNA at a particular developmental stage suggests protein function at that
stage
• Reverse transcriptase-polymerase chain reaction (RT-PCR) is quicker and more sensitive
• Reverse transcriptase is added to mRNA to make cDNA, which serves as a template for PCR
amplification of the gene of interest
• The products are run on a gel and the mRNA of interest identified
• Both methods are used to compare mRNA from different developmental stages
5. What is the purpose and method of a DNA
microarray assay?
• Automation has allowed scientists to measure expression
of thousands of genes at one time using DNA
microarray assays
• DNA microarray assays compare patterns of gene
expression in different tissues, at different times, or under
different conditions
Fig. 20-15
TECHNIQUE
1 Isolate mRNA.
2 Make cDNA by reverse
transcription, using
fluorescently labeled
nucleotides.
3 Apply the cDNA mixture to a
microarray, a different gene in
each spot. The cDNA hybridizes
with any complementary DNA on
the microarray.
Tissue sample
mRNA molecules
Labeled cDNA molecules
(single strands)
DNA fragments
representing
specific genes
DNA microarray
4 Rinse off excess cDNA; scan
microarray for fluorescence.
Each fluorescent spot represents a
gene expressed in the tissue sample.
DNA microarray
with 2,400
human genes
6. What is the purpose and method of in vitro
mutagenesis and RNA interference?
• One way to determine function is to disable the gene and observe the consequences
• Using in vitro mutagenesis, mutations are introduced into a cloned gene, altering
or destroying its function
• When the mutated gene is returned to the cell, the normal gene’s function might be
determined by examining the mutant’s phenotype
• Gene expression can also be silenced using RNA interference (RNAi)
• Synthetic double-stranded RNA molecules matching the sequence of a particular gene are
used to break down or block the gene’s mRNA
7. When studying humans, what is the purpose of looking
for a single nucleotide polymorphism? How does this aid
us in finding and tracking human genetic diseases?
• A single nucleotide polymorphism (SNP) is a single base pair site where a variation
is found in at least 1% of the population.
• Once a gene (especially disease genes) has been found to have a SNP shared by
affected people and not unaffected people, the gene is sequenced.
• The SNP and disease causing gene will most likely be inherited together because
they are close to each other on the genome. Therefore, the SNP can be used as a
marker for the disease.
• Doctors can perform a sensitive microarray analysis to look for SNPs or by PCR.
8. How much of the human genome doesn’t
code for a protein?
• 98% of the human genome does not directly code for proteins.