22 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
on completing the rst experiment!
Were you surprised at how much DNA you found in a
single strawberry? You added only a small amount of
DNA to the alcohol, and yet there was a lot of DNA. Now
consider all of the other food you eat - if the food was
at some point living, then it will have DNA in it - you
eat a lot of DNA on any given day!
Now that this experiment is complete, you won’t be
using your isolated DNA further. You can keep it or
throw it away. Since there are no dangerous or living

the toilet/sink and recycle or discard the tubes accord-
ing to your local rules.

several reasons:
It helped you begin your journey learning about
cells and molecule bonding
It helped you learn about how to break open cells,
which will be used later in this book to break open
cells that you have genetically engineered

following Fundamentals section, you should keep
remembering the DNA you saw.
Note that genetic engineers do use this technique to
isolate DNA from the environment to use in their proj-
ects. You’ll learn more about this as you become a
Genetic Engineering Hero!
In the following sections, you will take a more in-depth
look at the fundamentals of DNA, and how DNA relates
to cell survival. You’ll also be exploring how DNA can
change naturally or through human intervention. This
will set the stage for later chapters in which you will
start manipulating the genome of cells. Once you have
gone through the rest of this chapter, we recommend
that you go back and repeat the hands-on learning
exercise once more - not only will it reinforce what
youve learned, but you will start seeing strawberries,
soap, and salt in a way you never have before.
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23Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Fundamentals: DNA
Evolution: It’s natural for DNA to
change
All living organisms have DNA. DNA is like the blue-
print or the instructions for a living cell. As you’ll see
throughout this book, in addition to DNA, living cells
are packed full of “nano-machinery” that can read the
DNA and “execute its instructions.” The instructions
embedded in DNA are critical for the cell’s survival.
Cells and DNA can be compared to a computer and its
hard drive. The computer hard drive holds all the
information that is necessary to “run your computer.
The information is stored as tiny magnetic dots and
dashes in the hard disk. Like Morse code, the little
magnetic dots and dashes are the “language” that the
rest of the computer can understand. Perhaps the
most essential information on the hard drive is the
operating system, like Windows or Mac OS. This infor-

up what you see and hear when your computer boots
up, as well as the software that makes your keyboard,
mouse, screen, webcam, and microphone work. With-
out a hard drive, and the dot and dash information it
contains, your computer would not function.
The computer has many parts other than a hard drive.
These include your screen, keyboard, mouse, cooling
system, graphics, central processing units, battery,
and more. All of these “parts” together are required
to “bring your computer to life” when you press the
power button. The hard drive needs the other
computer parts so that the information stored on it
can be accessed, read, and executed. The computer
parts also need information on the hard drive so they
can operate and communicate with each other. By
changing the dot and dash information in the hard
drive, a computer can behave very differently. Over
the last 40 years, the operating systems of computers
have evolved substantially because they have been
-
opers.
DNA is simply a different medium for storing infor-
mation. Rather than tiny magnetic dots and dashes
on the hard disk, DNA is a microscopic string of tiny
molecules called nucleotides, and it is the order of the
nucleotides that make up the language that the cell
knows how to read. Also, just as the tiny magnetic

changed, so too can the string of molecules that make
up DNA. In other words, DNA can be altered.
In the natural world, DNA can spontaneously change
due to environmental factors, or due to cell malfunc-
tion. Environmental factors like ultraviolet light,
gamma radiation, chemicals in the environment,
viruses, and even molecules produced by other living
organisms can all have an “editing” affect on DNA.

can change how your computer operates (or whether
it will even turn on), a small change such as deleting
some DNA nucleotides can have a profound impact
on a living organism.

permanent chemical. While it is quite stable, DNA is

The changeability of DNA is the basis of evolution. It
is why every organism is unique and why there is
such a fantastic array of living organisms in the world
around you. For billions of years, the nucleotide
sequence making up the DNA of living cells has
changed time after time. DNA nucleotides are
constantly being erased, duplicated, inverted,
jumbled up, and combined with other organisms’
DNA. DNA molecules can even be copy-pasted and
cut-pasted through chemical reactions!
The genetic history of humans is a great example: Did

viruses that once infected our ancestors? An example
of a type of virus that can add its DNA to your genome

is a class of virus called retroviruses. HIV infects
human immune cells, then copies its nucleic acid into
human cells so that these human cells will keep this
new DNA and make more of the virus. This shows that
human DNA has not been solely human since “the
beginning.” Rather it is the accumulation of DNA from
different organisms in nature as well as natural
changes to the DNA sequence over time. When enough
DNA is transferred, duplicated, removed, or other-

and behaves differently from its parent.
It can take thousands, millions or billions of genera-
tions for changes in DNA to accumulate to the point
where an organism becomes unique. When minor
DNA changes happen even one thousand times, the
“Great-one-thousandth Grandparents” can look very
different than its “Great-one thousand Grandchild.” It
may even result in a different species! Let’s write this
out so you can see what 1000 generations look like:
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24 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
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great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great great great great great great
great great great great great great great great great great Grand Parent.
That is a lot of grandparents! Do you know who your
great-one thousand grandparents were? Do you think
they looked just like your grandparents? In humans,



in days. Considering that a microorganisms lineage
goes back billions of years, that provides a lot of
opportunities for generations to change and evolve.
Life on earth started with the simplest of life forms,
with simple DNA blueprints. Through billions of years
and an unimaginable number of incremental changes
to the DNA blueprint, we now see countless species of
microorganisms, plants, fungi, insects, and mammals
such as humans.
Modern Synthesis
While the understanding of DNA, genetics, and hered-
ity matured over hundreds of years, an essential
milestone occurred in the early 20th century as
Darwinian evolution and Mendelian genetics transi
-
tioned from theory to fact. The combining of
Darwinian evolution (natural selection) and Mende-
lian genetics (inherited DNA) was termed the Modern
Synthesis.
Today, Gregor Mendel is known as the founder of
genetics, and genetics, of course, is the foundation of
  

traits are passed on from one organism to the next,

traditional breeders of livestock and crops had been
slowly modifying organisms over at least thousands

that biology could be changed through domestication
had yet to be achieved.
It wasn’t until Mendel started his pea plants experi-
ments that crucial information on genetics emerged
(Figure 1-10). Mendel found that when he cross-polli-
nated pea plants with different colored seeds, some
of those seed colors were preferentially passed down
to the next generation of plants. But, looking further
down the line of pea plant generations, he found that
some seed colors eventually re-emerged! His experi-
      
experiments, went something like this:
1. Yellow seed pea plants were carefully bred with
other seeded yellow pea plants to ensure he had
“pure-breed” yellow pea plants.
2. The same was done with green seed pea plants.
3. Yellow and green seed pure-bred plants were
then carefully cross-pollinated. This is quite easy
to do. Today, you can use a Q-tip and gently rub a
blossom of one plant to gather pollen, then rub it
in another plant blossom, and lastly, rub it back

4. The plants grew, matured, and produced seeds
       
for similar future experiments.
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25Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
The pure-bred plants would always produce the
expected colored seeds: yellow produced yellow
seeds and green produced green seeds. However,


were yellow! It looked as though some genetic infor-
mation for yellow seeds was preferred over green
(Figure 1-11)!
But, things ended up getting a bit more complicated.
-
ation yellow seeds were grown into plants and
cross-bred? You might expect this preferential yellow
genetic information to cause only yellow seeds. But
the result included the reemergence of green seeds!
And the most interesting part was they appear in a
ratio of one green seed for every three yellow seeds.
       
derived information about how traits were passed
down from a parent to its offspring was available. It

rules” for which information is passed to the offspring.
To explain this, Mendel coined the terms “recessive”
and “dominant” genes. The green seeds were the
ones with the recessive trait and the yellow seeds the
dominant trait.
Mendel’s studies broadened beyond seed color into
different plant traits, including height, blossom
colors, pea pod shapes, colors, and more. In these
studies, he found other “genetic rules” existed! Today,
our hair color, eye color, skin color, and a lot more are
well-known examples of how genetics are passed
down from parents to offspring.
Modern synthesis combined Darwinian evolution
     

how biological organisms can change through time.
Mendelian genetics, now just genetics, turned out to
be the mechanism or the “how” and “why” different
genetic material is passed down from parent to
offspring. Darwinian evolution allowed scientists to
see that genetics applied to all organisms, not just pea
plants. Modern synthesis also included some other
key mechanisms in which DNA changes occur in
organisms and populations:
Mutations: when changes in the DNA sequence
happen due to copy errors. While mutations can be
increased due to environmental factors, this is
often considered independent of selective environ-
mental pressures (natural selection). In most cases,
mutations are harmful to an organism; however, in

that can help an organism survive in their environ-
ment. In other words, mutations do occur randomly
but can become a part of natural selection.
Random genetic drift: is where allele frequency
changes in populations. An allele is a DNA sequence
(e.g. gene) that is very similar to another allele but
has a slightly different sequence. Alleles are created
due to mutations. As organisms reproduce, these
different versions of DNA sequences will “move”
through a population. Similar to the pea experi-
ments above where the “yellow seed” and “green
seed” alleles “moved” through the pea population
as the plants were bred.
 is where allele frequency changes due
to immigration or emigration to/from a population.
For example, if there were only true-bred green
seed pea plants in a region and a person or bird
happened to bring a yellow pea seed to that region.
When that pea plant grows, its yellow seed allele
will become dominant in the region in the coming
years as cross-breeding occurs.
A key basis for natural selection, random genetic drift,

and result in different DNA sequences (alleles). While
most mutations negatively impact an organism, some

help an organism survive in a particular environment
(natural selection) or can help the organism survive
independent of the environment. The alleles can then
“move” around and change a population through gene
        
generation, mutations reshape us, and the world
around us as species change or new species emerge.
Figure 1-10.
Book _genetic engineering hero-AUG2021.indb 25Book _genetic engineering hero-AUG2021.indb 25 8/18/21 12:03 PM8/18/21 12:03 PM
26 Zero to Genetic Engineering Hero - Chapter 1 - Isolating DNA, the Blueprints of Life
Genetic engineering: The road to
precise editing of DNA

DNA in organisms for thousands of years through
domestication and selective breeding. You can see
the outcomes of these actions in our homes, farms,
and factories. These methods of changing the DNA of
living organisms take advantage of evolution. When
humans cross-breed plants, the DNA within the
plants mix: DNA from one plant will combine with


human intervention, however, if the new trait is bene-

for because the plant’s survival will be encouraged by
humans through watering, and propagating the
plant’s seeds. Because of this, plants, especially crop
-
able when compared to their ancestors (Figure 1-12).
Domestication and selective breeding do not only
apply to crops. Consider pets for a moment. The “orig-
inal dog” is Canis lupus, better known as the wolf. Dogs
have been so extensively bred by humans that a huge
dog such as a Great Dane—standing at a minimum of

physically mate and reproduce in nature with a small
dog such as a Chihuahua—standing at less than 1 foot
and weighing less than 10 pounds. The Chihuahua is

descendants from the same source DNA (Figure 1-13).
In the natural world, these two organisms can no
longer effectively breed. Their DNA can no longer
combine and intermix as would naturally happen in
a species. Without human intervention, this will
eventually lead to the development of two different
species. This is evolution in progress.
The methods in which humans evolve plants and pets
through deliberate breeding and selection extends
into all corners of the natural world - trees, grasses,

Much of the food we eat today was evolved through
selective breeding by humans. This process often
takes a long time because “DNA mixing” through
these methods is random, and desirable traits only
appear by chance. What if randomness could be taken
out of the equation? What if humans could, with
extreme precision, edit DNA?
The precise engineering of organisms is the focus of
this book. By its end, you will have gone through exer-
cises where you will have precisely changed an
organisms DNA to get a desired trait. Over the past
100 years, humans have made ground-breaking
discoveries that have led us to understand what DNA
is, how DNA behaves, and its importance in biology.
These discoveries have led to new technologies that
enable us to precisely read, write and edit the DNA of
organisms. There has also been a change in the mind-
set of people. No longer is nature and the natural
world seen as being immovable or unchangeable. A
robust engineering discipline has emerged where we
can now make very important things using biology.
We call this the Biology-as-a-Technology mindset.
The knowledge and skills imparted by this book are
not to be taken lightly. Understanding how DNA and
cells interact will be vital to making informed deci-
sions about using your new skills. Now that you have
seen DNA and know that it can be manipulated let’s
further explore the building blocks of DNA and the
cells where they reside.
Figure 1-11. Mendels pea plants experiment provided the
basis for modern genetics.
Book _genetic engineering hero-AUG2021.indb 26Book _genetic engineering hero-AUG2021.indb 26 8/18/21 12:03 PM8/18/21 12:03 PM
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