Biology: Applied Genetics and Biotechnology notes
(revised 11/2009)
Selective Breeding—increasing “good” alleles in an organism’s population by breeding individuals with desired traits.
Inbreeding—mating between closely related individuals. This practice is used in animal husbandry (show dogs, race horses,
farm animals, etc.) to insure that many desired traits show consistently in individual organisms. However, inbreeding also
increases the chances of harmful recessive traits occurring. Biology mythbuster: inbreeding does NOT directly lead to mental
retardation; many people think this but research does not support it.
Hybrids—organisms created by crossing parents that were purebred for different traits.
Hybrid plants and animals are often bigger, stronger and more productive than purebred plants. This is called “hybrid vigor”.
In order to breed plants or animals in a controlled manner, the genotype of the organism must be determined. Organisms that are
not pure for a trait produce a variety of different phenotypes, whether they are desired or not.
Genetic Engineering
Genetic engineering—a method of cutting a desired piece of DNA from one organism and inserting it into another.
Recombinant DNA—the DNA that is made by connecting (recombining) fragments of DNA from different sources.
Transgenic organisms—organisms that have functional pieces of DNA from other organisms in them.
Restriction enzymes—bacterial proteins that cut DNA at specific points in the nucleotide sequence. Hundreds of different
restriction enzymes exist.
Gel electrophoresis—fragments of DNA are separated by size by passing them through a gel that has electric current running
through it. Negatively charges pieces of DNA move from wells at one end towards the positive electrode at the other. Small
fragments move farthest, large fragments move least. The process is similar to paper chromatography (used in the chlorophyll
pigment lab).
Vectors—anything used to carry DNA into a new organism.
TYPES of vectors
Mechanical
Micropipette—tiny needle-like pipette injects DNA into a cell.
DNA bullet—tiny DNA coated bullet is shot into a cell with an air gun.
Biological
Viruses—viruses that have desired pieces of DNA in them can transfer the foreign DNA into a new organism.
Plasmid—a circular piece of bacterial DNA can carry the foreign DNA into a new organism.
Cloning—making genetically identical copies of DNA.
Gene cloning
When a piece of DNA has been introduced into a new species, that foreign DNA will be reproduced every time the new cell
divides. Transferring human DNA to bacterial DNA can result in millions of copies made in a short time. Currently this only
works for short pieces of human DNA.
Reproductive cloning
Cloning one gene is much simpler than cloning an animal’s entire genome. Dolly the cloned sheep (1996) was created by taking
an udder cell (any 2n cell should work) from an adult sheep and fusing it with an egg cell that had its nucleus removed (called
“enucleated”.) The enucleated egg cell has no DNA. The DNA from Dolly’s udder cell became the egg cell’s DNA. The fused
egg was implanted back into a surrogate mother (intentionally not the cell donor sheep to prove the clone was not like the
surrogate), and Dolly developed normally from there. Cows (@UConn), pigs, mice, monkeys and a horse (only true clone since
cell donor was also the surrogate mother) have been cloned. Reproductive cloning success (<0.5% births per attempt) has not
improved in 13 years since Dolly and has almost been abandoned completely except...Big news: Scientists have the entire
genome of the woolly mammoth (gotten from a frozen mammoth carcass, 2008). They found out the Asian elephant is its closest
living relative and plan to clone a mammoth with an Asian elephant as surrogate mother. Stay tuned!
DNA sequencing
Cloning billions of sections of DNA allows the sequence of DNA to be determined. This technique allows genome sequencing
(see Human Genome Project)
Uses for recombinant bacteria (gene clones grown in bacteria)
Industry
 Used to clean up oil spills. The bacteria “eat” the oil and break it down into harmless substances.
 Being developed to extract minerals from ore (bacteria “eat” the ore, leave the minerals.)
Medicine
 Produce insulin to treat diabetes, and human growth hormone used to treat dwarfism.
 Used to produce phenylalanine that is used to make aspartame (Nutra-sweet®).
Agriculture
 Bacteria prevent frost damage in strawberries, and produce nitrogen fertilizer for plants.
Uses for transgenic organisms (also called GMO’s or genetically modified organisms)
Plants
 Have been engineered to resist herbicides, resist pests, and to increase the protein or vitamin content of the plant (e.g. golden
rice has vitamin A. Corn, cotton and soybeans in U.S. are GMO for herbicide resistance, natural pest resistance and
increased nutrition.
Animals
 Animals have been created with human diseases, so the cure for those diseases might be found without excessive human
testing. Mice given human Huntington’s disease and Alzheimer’s have led to breakthroughs in treatments.
 Pigs (milk and chickens soon) with omega-3 fatty acids (good for the heart). The natural source of omega-3 fatty acids is
some oily fishes like tuna and salmon, but they are overharvested and often have high mercury levels in them.
 Glo-fish—the gene for gfp (green fluorescent protein) from a jellyfish was added to create a novelty pet. Not as wellknown, (but way more important) this discovery led to a Nobel Prize (Shimomura, Chalfie, Tsien 2008) since the gene is tacked
on to other GM attempts, allowing visual proof of cells that got the new gene being studied.
The Human Genome
Genome—the complete set of genes for an organism.
The human genome contains approximately 20,000-23,000 genes, made up of about 3 billion base pairs. (ATACGACCTG, etc.,
3 billion times!) All bases have been sequenced (as of 2001) but exactly what each gene is or does isn’t yet known. Up until
2001, it was thought that the human genome might contain around 100,000 genes because that is about how many different
proteins are in humans. Scientists now know that many genes can make more than one kind of protein (the same sequence is
edited in different ways). 98.5% of the 3 billion pairs are “junk” (do NOT code for any proteins); why this is, is still mostly
unknown. Many scientists’ first guess was that the “junk” is old viruses that have infected the genome over the billion years it
has evolved. MicroRNA (miRNA) and other gene control factors are recently known to be coded for by the “junk”.
How did they do it?
In order to sequence genes, thousands of copies (clones) of the gene are needed. A technique called PCR (polymerase chain
reaction) allowed machines to clone DNA. The process involves heating and cooling DNA fragments (to unwind them) and
using DNA polymerase enzyme to induce natural replication. The problem is that most enzymes can’t be heated and cooled
without breaking down. PCR works because an American scientist Dr. Kary Mullis (Nobel Prize 1993) had the simple, brilliant
idea to use DNA polymerase enzyme from bacteria that survive in hot springs in Yellowstone NP. (For his great discovery, Dr.
Mullis received a $10,000 bonus from the company he was working for. The company sold the technology for $300,000,000!
Not surprisingly, Kary Mullis doesn’t work there any more and is more than a bit “disgruntled.”)
The copies are then cut with restriction enzymes. Each clone is cut so that it is one base shorter than the other. That way, the
last base on each piece is known. The pieces are then sorted by “tagging” the last base in the piece with a different colored dye
(i.e. yellow for T and red for A, etc.) and the order is determined.
Why bother? The human DNA sequence is used for a variety of applications scientists thought impossible just 30 years ago.
Current (or very near future) uses:
 Diagnosing genetic disorders accurately before birth.

Making normal genes for “gene therapy”. Gene therapy involves inserting normal genes (by using a vector) into a human
cell to treat disorders. Recent breakthroughs: cure red-green colorblindness in primates, restore vision to a boy blind from
birth with Leber’s Congenital Blindness, halt progression of Alzheimer’s disease and restore some nerve function by
introducing NGF (nerve growth factor) to patients’ cells.

Giving cell cultures a genetic disease so the cells not a whole test organism can be studied for a disease cure. Less lab rats,
monkeys, etc. that need to be harmed in search for a cure. Only promising treatments will go o to further testing.

DNA “fingerprinting”. Because every person’s DNA is unique, it is the best way to identify suspects from crime scene
evidence. DNA from a crime scene can be matched to a suspect’s DNA with almost 100% certainty (more than 1,000
known “markers” or potential match points), even better than traditional fingerprints which only uses 7 matching factors.
Future (in your lifetime) uses (currently these are still in research, but theoretically possible soon):
 Cure many forms of cancer, AIDS, CF, MD, sickle cell and other diseases that involve specific changes to normal
genes. Replacing the “bad” gene with a normal gene works for some treatments already, so more will be here soon.

By knowing what genes cause certain side effects with medicines, pharmacists can provide individualized medicines
that will work as close to 100% efficiently as possible for each person’s specific genetic make-up.