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Essentials of the Living World
Second Edition
George B. Johnson
Jonathan B. Losos
Chapter 14
The New Biology
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
14.1 Genomics
• Genomics is a field that compares the
entire DNA content of different organisms
 the genome is the full complement of genetic
information of an organism (i.e., all of its
genes and other DNA)
 DNA sequencing is a process that allows
scientists to read each nucleotide in a strand
of DNA
Table 14.1 Some Eukaryotic Genomes
14.1 Genomics
• In DNA sequencing, a fragment of DNA is
first amplified so that there are thousands
of copies
• Next, these fragments are then mixed with
copies of DNA polymerase, primers, a
supply or nucleotide bases and a supply of
four different chain-terminating tags
 the chemical tags form complementary base
pairs just like the nucleotide bases
14.1 Genomics
• Heat is applied to denature the double-stranded
DNA fragments and then cooled to allow for the
primer to bind to a single strand of DNA
• DNA polymerase synthesizes a complementary
strand until a chemical tag is incorporated
 because of the relatively low concentration of
chemical tags compared with the nucleotides, the
mixture will contain a series of double-stranded DNA
fragments of varying lengths
14.1 Genomics
• The fragments of DNA are then separated
according to size by gel electrophoresis
 the fragments become arrayed in order and
the sequence of nucleotides can be read off
one nucleotide at a time
• DNA sequencing is now automated and
can handle large numbers of samples
 this has made possible the sequencing of
large eukaryotic genomes
Figure 14.1 How to sequence DNA
14.2 The Human Genome
• The publication of the sequence of the
entire human genome occurred on June
26, 2000
 the human genome contains more than 3
billion base pairs
 it is estimated that there are between 20K and
30K protein-encoding genes
Figure 14.2 The human genome
14.2 The Human Genome
• Four classes of protein-encoding genes are
found in the human genome
 single-copy genes
• found in only one copy at a particular location on a
chromosome
 segmental duplications
• blocks of genes that have been copied over from one
chromosome to another
 multi-gene families
• groups of related but distinctly different genes
 tandem clusters
• repeated genes that are repeated thousands of times in a
tandem array
14.2 The Human Genome
• There are four major types of non-coding DNA
 noncoding DNA within genes
• these are introns
 structural DNA
• tightly coiled DNA that remains untranscribed
• called heterochromatin
 repeated/duplicated sequences
• simple sequence repeats (SSRs) that are scattered about
chromosomes
 transposable elements
• bits of DNA that jump from one location on a chromosome to
another
Table 14.2 Types of DNA Sequences
Found in the Human Genome
14.3 A Scientific Revolution
• Genetic engineering is moving genes from one
organism to another
 the first stage in a genetic engineering experiment is
to chop up the source DNA and obtain a copy of the
gene you want to transfer
 restriction enzymes bind to specific short sequences
on the DNA and make a specific cut
• the sequence is symmetrical
• the cut generates DNA fragments that are “sticky” because
the incision made by the restriction enzyme is made to the
side
14.3 A Scientific Revolution
• DNA from another source that is cut with
the same restriction enzyme will have the
same sticky ends
 these ends can be joined together by the
enzyme ligase
• Restriction enzymes are the basic tools of
genetic engineering
Figure 14.4 How restriction enzymes
produce DNA fragments with sticky ends
14.3 A Scientific Revolution
• The source of DNA to be transferred is
often a DNA library, a collection of DNA
fragments representing all of the DNA from
an organism
• Prior to transfer, a genetic engineer needs
a vehicle to carry the source DNA into the
host cell
14.3 A Scientific Revolution
•
A gene transfer experiment occurs in four stages
1.
Cleaving DNA
•
2.
Producing recombinant DNA
•
3.
placing the DNA fragments into vectors and then transferring the
DNA into the target cells
Cloning
•
4.
cutting the source and vector DNA
introducing DNA-bearing vectors into target cells and then
allowing the target cells to reproduce
Screening
•
selecting the particular infected cells that have received the gene
of interest
Figure 14.5 How a genetic
engineering experiment works
14.4 Genetic Engineering and
Medicine
• Much of the excitement about genetic
engineering has focused on its potential to
improve medicine, to aid in curing and
preventing illness
• Advances have been made in the following
areas
 the production of proteins used to treat illness
 the creation of new vaccines to combat infection
 the replacement of defective genes (i.e., gene
therapy)
14.4 Genetic Engineering and
Medicine
• Many genetic defects occur because our
cells fail to make critical proteins
 an example is diabetes
• diabetics cannot control their blood sugar levels
because a critical protein, insulin, is not made
• this failure can be overcome by receiving a
donation of protein made by another body
• through genetic engineering, the genes encoding
insulin have been introduced in bacteria, which
can cheaply produce large quantities of protein
Table 14.3 Genetically Engineered Drugs
14.4 Genetic Engineering and
Medicine
• Genetic engineering is also used to create subunit
vaccines against viruses, such as herpes and hepatitis
 engineers splice genes from the coat of the virus into a fragment
of cowpox (vaccinia) virus genome
 the smallpox virus is used as a vector to carry the viral coat
genes into cultured mammalian cells, where the immune system
can develop an immunity to the virus prior to being exposed to a
fully active virus
 this method of using one virus as a vector to introduce fragments
of the DNA of a disease-causing virus produces what are called
piggyback vaccines
Figure 14.7 Constructing a subunit, or piggyback,
vaccine for the herpes simplex virus
14.5 Genetic Engineering and
Agriculture
• Genetic engineering of crop plants has
successfully
 made plants more resistant to disease
 improved nutritional content and yield
 made crops hardier and better able to resist
environmental stresses
14. 5 Genetic Engineering and
Agriculture
• Engineering crops to be resistant to insect
pests reduces the need to add insecticides
to the environment
 for example, genes from the soil bacterium,
Bacillus thuringiensis (Bt), that produces a
protein that is toxic when eaten by crop pests
have been inserted into the chromosomes of
tomatoes
• because the plants can synthesis Bt protein, they
are toxic to pests, such as the tomato hornworm
14.5 Genetic Engineering and
Agriculture
• Herbicide resistance has also been
genetically engineered
 glyphosphate is a powerful herbicide that
kills most actively growing plants and is used
to control weeds
 using a gene gun, engineers inserted an
isolated gene from a bacterium that is
resistant to glyphosphate into crop plants
• the glyphosphate can now be widely applied to
fields and orchards where it retards weed growth
but not crop growth
Figure 14.8 Shooting genes into cells
Figure 14.9 Genetically engineered
herbicide resistance
14.5 Genetic Engineering and
Agriculture
• The real promise of genetically modified
(GM) plants is to produce crops with
desireable traits that directly benefit the
consumer
 for example, to combat iron and vitamin A
micronutrient deficiencies among the world’s
rice eaters, genetic engineers created GM
“golden” rice
• this transgenic rice contains genes from a bean, a
fungus, wild rice, and a daffodil to increase its
nutritional value
Figure 14.10 Transgenic “golden”
rice
14.5 Genetic Engineering and
Agriculture
• Genetic engineering has been the cause of
considerable controversy and protest
• Bioengineers modify crops in two major ways
 the modification makes the crop easier to grow
 the modification improves the food itself
• Is eating GM food dangerous?
 does adding genes introduce novel proteins that
maybe potentially harmful when consumed?
 could introduced proteins become allergens?
14.5 Genetic Engineering and
Agriculture
• Those concerned about the widespread use of GM crops
raise three concerns concerning their effects on the
environment
 possibility of unintentional harm to other organisms
• weeds might be important sources of food and shelter for non-pest
insects
 potential for new resistance
• pests might be likely to become resistant to the engineered proteins
• farmers are required to plant some non-GM crop alongside the GM
crop in order to slow the selection pressure for resistance
 gene flow beyond the intended target by gene flow
• modified genes may spread to non-GM species due to interbreeding
Inquiry & Analysis
• Does the gene conferring
resistance pass to other
plants of this species, A.
stolonifera? to individuals
of the related species A.
gigantea?
• Is it fair to conclude that
genetically modified traits
can pass from crops to
other plants?
Graph of Frequency of Sentinel Plants
14.6 Reproductive Cloning
• Theory of irreversible determination
states that animal cells become
irreversibly committed after the first cell
divisions of the developing embryo
 nuclear transplants involve the transplanting
of a nucleus from an animal cell into the an
enucleated egg and seeing if it develops
• only cells extracted from early embryos (no further
than the 16-cell stage) will develop into an adult
• we now know that this theory is WRONG
14.6 Reproductive Cloning
• Keith Campbell, a geneticist, proposed
that, in order for a successful nuclear
transplant to take place, both the egg and
the donated nucleus need to be in the
same stage of the cell cycle
 by first starving the cell so that they paused at
the G1 checkpoint, the nuclear transfers
succeeded in producing cloned farm animals
14.6 Reproductive Cloning
• Reproductive biologist Ian Wilmut worked with
Campbell to clone a sheep using the mammary
cells of an adult
Figure 14.12 Wilmut’s animal cloning experiment.
14.6 Reproductive Cloning
Figure 14.12 Wilmut’s animal cloning experiment.
Figure 14.13 A parade of cloned critters
14.6 Reproductive Cloning
• Despite the success of “Dolly the Sheep,”
only a small fraction of transplanted
embryos survive to term
 most embryos will die late in pregnancy
 many exhibit large offspring syndrome or
lateral developmental problems as they
become adults
 almost none survive to a normal lifespan
14.6 Reproductive Cloning
• What may be wrong with cloned embryos is that
as mammalian eggs and sperm mature, their
DNA is conditioned by the parent by
reprogramming
 this reprogramming is really a form of genetic
imprinting which affects the ability of a gene to be
read
• some genes are permanently turned off, such as by
methylation, in which a –CH3 group is attached to a gene so
that polymerase cannot read it
• other genes may be turned on by methylating a regulatory
sequence that had prevented its transcription
14.6 Reproductive Cloning
• Precise genomic imprinting is required for
normal development
 gametic imprinting
• genomic imprinting that takes place in adult reproductive
tissue
 zygotic imprinting
• occurs after the egg has been fertilized and the egg’s
cytoplasm reprograms the DNA introduced by the sperm
• cloning often fails because there is not enough time for
zygotic imprinting before the egg starts to divide
Figure 14.14 Two forms of genomic
imprinting
14.7 Embryonic Stem Cells
• Embryonic stem cells are special cells
that form early in development and each
has the capacity to develop into a healthy
individual
• Totipotent is the ability of cells, such as
stem cells, to have the ability to form any
body tissue, and even an adult animal
Figure 14.15 Human embryonic
stem cells (x 20)
14.7 Embryonic Stem Cells
• As development proceeds, some of the
embryonic stem cells begin to become
committed to forming a certain type of
tissue only
 every major tissue is formed from its own
tissue-specific adult stem cell
• Because they can develop into any tissue,
embryonic stem cells offer the exciting
possibility of restoring damaged tissues
Figure 14.16 Using embryonic stem
cells to restored damaged tissue
14.8 Therapeutic Cloning
• Therapeutic cloning (also called somatic cell nuclear
transfer) address the issue of immune acceptance of a
transplanted cell used for therapy
 in therapeutic cloning, the cloned embryo is destroyed to harvest
embryonic stem cells, which will be automatically tolerated by
the recipient of the therapy
 in contrast, in reproductive cloning, the cloned embryo is allowed
to develop into adults
 there are many ethical issues involved with using these
therapies with human embryos
Figure 14.18 How human embryos
might be used for therapeutic cloning
14.9 Gene Therapy
• Gene transfer therapy involves
introducing “healthy” genes into cells that
lack them
 early work with a cold virus vector, called an
adenovirus, was unsuccessful in humans
because of immune attack
 a new vector, adeno-associated virus (AAV)
does not elicit a strong immune response and
seems promising
Figure 14.19 Using gene therapy to cure a
retinal degenerative disease in dogs
Inquiry & Analysis
• Judging by visual similarity,
which adult dog is the closer
relative of Snuppy?
• The scientist who cloned
Snuppy has been accused of
faking research evidence in
different experiments
concerning stem cells.
• Given this cloud on his
reputation, what evidence
would you accept that Snuppy
is indeed a clone?
Picture of Snuppy