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Unit 3
Understanding and Manipulating
Genomes
One of the greatest achievements of modern science
Has been the sequencing of the human genome, which
Recombinate
bacterium
3 3 Host cell grown in culture,
2 Plasmid put into
to form a clone of cells
bacterial cell
containing the “cloned”
gene of interest
Gene of
Protein expressed
interest
by gene of interest
Copies of gene Protein harvested
Basic Basic
research research
on gene 4 Basic research and on protein
various applications
Gene for pest Gene used to alter Protein dissolves Human growth
resistance inserted bacteria for cleaning blood clots in heart hormone treats
into plants up toxic waste attack therapy stunted growth
Tools of Genetic Engineering (pg 143)
1. DNA Polymerase
2. Restriction enzymes (restriction
endonucleases)
3. DNA Ligase
4. Reverse Transcriptase
Using Restriction Enzymes to Make
Recombinant DNA
There are 2 type of restriction enzymes / nucleases – Deoxyribonucleases (DNAse)
and Ribonucleases (RNAse) that can cut/digest DNA and RNA respectively.
These nuclease can be subdivided into exonucleases and endonucleases.
Exonucleases digest DNA and RNA from their terminal ends while endonucleases
digest from within the DNA and RNA molecules.
For genetic engineering, the type commonly used to cut DNA is restriction
endonuclease.
Restriction endonuclease were discovered in the 1960s and they protect bacterial
cells by cutting up foreign DNA from other organisms or bacteriophages.
Restriction enzymes
or blunt ends.
The most useful restriction enzymes like EcoRI cleave / cut DNA in
a staggered way
Producing fragments with “sticky ends” that can bond with
DNA 5 GAATTC 3
3 CTTAAG
5
3 DNA ligase
seals the strands. Recombinant DNA molecule
Cloning of Eukaryotic genes (pg 143)
Cloning eukaryotic genes into bacterial cells using DNA sequences
is particularly challenging because of incompatibility between
eukaryotic and prokaryotic biochemical machinery.
The enzyme, Reverse transcriptase, can be used to make a gene
from mRNA sequences instead.
mRNA sequences are generally used for cloning because they
have already undergone RNA processing and can be easily
isolated.
Reverse transcriptase enzymes are isolated from retroviruses and
can be used to produce a single complementary copy of DNA
(cDNA) based on mRNA sequences.
This single strand of cDNA can then be used as a template by the
enzyme DNA Polymerase to synthesize another complementary
DNA strand resulting in double stranded DNA which can then be
inserted into a vector for cloning.
Cloning a Eukaryotic Gene in a
Bacterial Plasmid
In gene cloning, the original plasmid is called a cloning vector
Defined as a double stranded circular DNA molecule aside from the
bacterial chromosome that can carry foreign DNA into a cell and replicate
independently on its own.
Bacterial plasmids are widely used as cloning vectors for several reasons:
they can be easily isolated from bacterial cells; manipulated to form
recombinant plasmids via insertion of foreign DNA; the recombinant
plasmids can be reintroduced into bacterial cells and they can replicate
rapidly.
Producing Clones of Cells
APPLICATION Cloning is used to prepare many copies of a gene of interest for use in sequencing the
gene, in producing its encoded protein, in gene therapy, or in basic research.
TECHNIQUE In this example, a human gene is inserted into a plasmid from E. coli. The plasmid contains
the ampR gene, which makes E. coli cells resistant to the antibiotic ampicillin. It also contains
the lacZ gene, which encodes -galactosidase. This enzyme hydrolyzes a molecular mimic of
lactose (X-gal) to form a blue product. Only three plasmids and three human DNA fragments
are shown, but millions of copies of the plasmid and a mixture of millions of different human
DNA fragments would be present in the samples.
1 Isolate plasmid DNA and human DNA. Bacterial cell lacZ gene
(lactose Human
breakdown) cell
Restriction
2 Cut both DNA samples with the same restriction site
enzyme ampR gene
(ampicillin Bacterial Gene of
resistance) plasmid interest
Sticky
3 ends Human DNA
Mix the DNAs; they join by base pairing. fragments
The products are called recombinant plasmids
Bacterial
clone
RESULTS Only a cell that took up a plasmid, which has the ampR gene, will reproduce and form
a colony. Colonies with non-recombinant plasmids will be blue, because they can
hydrolyze X-gal. Colonies with recombinant plasmids, in which lacZ is disrupted, will be
white, because they cannot hydrolyze X-gal. By screening the white colonies with a
nucleic acid probe (see Figure 20.5), researchers can identify clones of bacterial cells
carrying the gene of interest.
Identifying Clones Carrying a Gene of
Interest
Hybridization
on filter
3 The filter is laid under
1 A special filter paper is
2 The filter is treated to break photographic film, 4 After the developed film
pressed against the is flipped over, the
open the cells and denature allowing any
master plate, reference marks on the
their DNA; the resulting single- radioactive areas to
transferring cells to film and master plate are
stranded DNA molecules are expose the film
the bottom side of the aligned to locate colonies
treated so that they stick to (autoradiography).
filter. carrying the gene of interest.
the filter.
RESULTS Colonies of cells containing the gene of interest have been identified by nucleic acid hybridization. Cells from
colonies tagged with the probe can be grown in large tanks of liquid growth medium. Large amounts of the DNA
containing the gene of interest can be isolated from these cultures. By using probes with different nucleotide
sequences, the collection of bacterial clones can be screened for different genes.
Storing Cloned Genes in DNA Libraries
(Genomic Library)
A genomic library made using bacteria
Is the collection of recombinant vector clones produced by
cloning DNA fragments derived from an entire genome
Foreign genome
cut up with
restriction
enzyme
or
Bacterial Recombinant
Recombinant
clones plasmids Phage
phage DNA
clones
RESULTS After the current is turned off, a DNA-binding dye is added. This dye
fluoresces pink in ultraviolet light, revealing the separated bands to which it
binds. In this actual gel, the pink bands correspond to DNA fragments of
different lengths separated by electrophoresis. If all the samples were initially
cut with the same restriction enzyme, then the different band patterns indicate
that they came from different sources.
Restriction fragment analysis
Is useful for comparing two different DNA molecules, such
as two alleles for a gene
Normal -globin allele
Large
fragment
376 bp
201 bp
175 bp
TECHNIQUE In this example, we compare genomic DNA samples from three individuals: a homozygote
for the normal -globin allele (I), a homozygote for the mutant sickle-cell allele (II), and a
heterozygote (III).
Heavy
Restriction Nitrocellulose weight
DNA + restriction enzyme
fragments paper (blot)
I II III
Gel
Sponge
Paper
I Normal II Sickle-cell III Heterozygote Alkaline towels
-globin allele solution
allele
1 Preparation of restriction fragments. 2 Gel electrophoresis. 3 Blotting.
Probe hydrogen-
bonds to fragments
containing normal
or mutant -globin I II III
Radioactively I II III
labeled probe
for -globin
gene is added Fragment from
to solution in sickle-cell Film over
a plastic bag -globin allele paper blot
Fragment from
Paper blot normal -globin
1 Hybridization with radioactive probe. allele 2 Autoradiography.
RESULTS Because the band patterns for the three samples are clearly different, this method can be used to
identify heterozygous carriers of the sickle-cell allele (III), as well as those with the disease, who have
two mutant alleles (II), and unaffected individuals, who have two normal alleles (I). The band patterns
for samples I and II resemble those observed for the purified normal and mutant alleles, respectively,
seen in Figure 20.9b. The band pattern for the sample from the heterozygote (III) is a combination
of the patterns for the two homozygotes (I and II).
Restriction Fragment Length Differences as
Genetic Markers
Restriction fragment length polymorphisms (RFLPs)
Are differences in DNA sequences on homologous
chromosomes that result in restriction fragments of different
lengths
Specific fragments
Can be detected and analyzed by Southern blotting
The thousands of RFLPs present throughout eukaryotic DNA
Can serve as genetic markers
Mapping
Entire genomes can be mapped at the DNA
level
The Human Genome Project
Sequenced the human genome
Scientists have also sequenced genomes of
other organisms
Providing important insights of general biological
significance
Genetic (Linkage) Mapping: Relative
Ordering of Markers
The initial stage in Cytogenetic map Chromosome
genome
Genes located
hybridization (FISH)
by FISH
1 Genetic (linkage)
Is to construct a mapping
Ordering of genetic
markers such as RFLPs,
linkage map of
simple sequence DNA,
and other polymorphisms
Genetic
(about 200 per chromosome)
markers
several thousand
genetic markers
2 Physical mapping
Ordering of large over-
lapping fragments
spaced throughout
cloned in YAC and BAC
vectors, followed by
ordering of smaller Overlapping
fragments
each of the
fragments cloned in
phage and plasmid
vectors
complementary to the original DNA fragment. Each DNA (template Labeled strands 3
strand starts with the same primer and ends with a 5 C ddG
strand) ddA A
T
dideoxyribonucleotide (ddNTP), a modified G ddC C C
ddT T T T
nucleotide. Incorporation of a ddNTP terminates a A
C ddG G G G G
growing DNA strand because it lacks a 3’—OH group, T
ddA
ddA A
A
A
A
A
A
A A
A
T A A
the site for attachment of the next nucleotide (see C ddG G G G G G G G
C C C C C C C C
Figure 16.12). In the set of strands synthesized, each G
A
ddC
T T T T T T T T
T
nucleotide position along the original sequence is C G
G
T
G
T
G G
T
G
T
G G G
T
A T T T
T
represented by strands ending at that point with the 3 A T
T T T T T T T T
complementary ddNT. Because each type of ddNTP
Direction
is tagged with a distinct fluorescent label, the identity of movement
of the ending nucleotides of the new strands, and of strands
ultimately the entire original sequence, can be
determined.
CGCCATCAGT ACGATACTGGT
4 Order the AGTCCGCTATACGA
sequences into one
overall sequence
with computer
software.
…ATCGCCATCAGTCCGCTATACGATACTGGTCAA…
Genome sequences provide clues to
important biological questions
In genomics
Scientists study whole sets of genes and their
interactions
Identifying Protein-Coding Genes in
DNA Sequences
Computer analysis of genome sequences
Helps researchers identify sequences that are likely to encode proteins
Current estimates are that the human genome contains about
25,000 genes
But the number of human proteins is much larger
Comparison of the sequences of “new”
genes
With those of known genes in other species may
help identify new genes
Determining Gene Function
For a gene of unknown function
Experimental inactivation of the gene and
observation of the resulting phenotypic effects
can provide clues to its function
Studying Expression of Interacting
Groups of Genes
DNA microarray assays allow researchers
to compare patterns of gene expression
In different tissues, at different times, or under
different conditions
DNA microarray assay of gene expression levels
APPLICATION With this method, researchers can test thousands of genes simultaneously to
determine which ones are expressed in a particular tissue, under different environmental conditions Tissue sample
in various disease states, or at different developmental stages. They can also look for coordinated
gene expression.
TECHNIQUE
mRNA molecules
1 Isolate mRNA.
4 Rinse off excess cDNA; scan microarray for fluorescence. Each fluorescent DNA
spot (yellow) represents a gene expressed in the tissue sample. microarray
RFLP marker
DNA
Restriction Disease-causing
sites allele
Normal allele
Human Gene Therapy
Gene therapy
Is the alteration of an afflicted individual’s genes
Holds great potential for treating disorders
traceable to a single defective gene
Uses various vectors for delivery of genes into cells
Cloned gene
(normal
allele,
absent 1 Insert RNA version of normal allele
from into retrovirus.
patient’s
cells) Viral RNA
Gene therapy 2
using a Retrovirus
capsid
2 Let retrovirus infect bone marrow cells
that have been removed from the
retroviral vector patient and cultured.
4 Inject engineered
cells into patient.
Pharmaceutical Products
Applications of DNA technology include
Large-scale production of human hormones and
other proteins with therapeutic uses
Production of safer vaccines
Forensic Evidence
DNA “fingerprints” obtained by analysis of tissue
or body fluids found at crime scenes
Can provide definitive evidence that a suspect is guilty or
not
DNA fingerprinting
Can also be used in establishing paternity
Blood from
Defendant’s defendant’s Victim’s
blood (D) clothes blood (V)
A DNA 4 g 8 g
D Jeans shirt V
fingerprint
Is a specific
pattern of bands
of RFLP markers
on a gel
Environmental Cleanup
Genetic engineering can be used to modify
the metabolism of microorganisms
So that they can be used to extract minerals from
the environment or degrade various types of
potentially toxic waste materials
Agricultural Applications
DNA technology
Is being used to improve agricultural productivity
and food quality
Animal Husbandry and “Pharm”
Animals
Transgenic animals
Contain genes from other organisms
Have been engineered to be pharmaceutical “factories”
Genetic Engineering in Plants
Agricultural scientists
Have already 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
Agrobacterium tumefaciens
APPLICATION Genes conferring useful traits, such as pest resistance, herbicide resistance,
delayed ripening, and increased nutritional value, can be transferred from one
plant variety or species to another using the Ti plasmid as a vector. Ti
plasmid
TECHNIQUE
Site where
restriction
enzyme cuts
1 The Ti plasmid is isolated from the bacterium Agrobacterium
tumefaciens. The segment of the plasmid that integrates into
T DNA
the genome of host cells is called T DNA. DNA with
the gene
of interest
Recombinant
2 Isolated plasmids and foreign DNA containing a gene of Ti plasmid
interest are incubated with a restriction enzyme that cuts in
the middle of T DNA. After base pairing occurs between
the sticky ends of the plasmids and foreign DNA
fragments, DNA ligase is added. Some of the resulting
stable recombinant plasmids contain the gene of interest.
RESULTS Transformed cells carrying the transgene of interest can regenerate Plant with
complete plants that exhibit the new trait conferred by the transgene. new trait
Safety and Ethical Questions Raised
by DNA Technology
The potential benefits of genetic
engineering
Must be carefully weighed against the potential
hazards of creating products or developing
procedures that are harmful to humans or the
environment
Today, most public concern about possible
hazards
Centers on genetically modified (GM) organisms
used as food